id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_cons_00079 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000789.4(ACE):c.21_30del (p.Arg8fs) (in gene ACE), classify the evolutionary constraint across the variant's genomic window. | NM_000789.4(ACE):c.21_30del (p.Arg8fs) VARIANT_IN_GENE ACE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000789.4(ACE):c.21_30del (p.Arg8fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000789.4(ACE):c.21_30del (p.Arg8fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000789.4(ACE):c.21_30del (p.Arg8fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 63477109,
"track": "phyloP100way",
"window": 20,
"scores": [
2.9706900000000003,
... | [
{
"source_db": "ClinVar",
"source_id": "ACE",
"text": "NM_000789.4(ACE):c.21_30del (p.Arg8fs) VARIANT_IN_GENE ACE",
"confidence": 1
}
] | {
"variant": "NM_000789.4(ACE):c.21_30del (p.Arg8fs)",
"gene": "ACE",
"mean_phylop": 0.312,
"track": "phyloP100way"
} | 1 |
co_cons_00080 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 10q26.13-26.3(chr10:124988334-135427143)x3 (in gene ABRAXAS2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 10q26.13-26.3(chr10:124988334-135427143)x3 VARIANT_IN_GENE ABRAXAS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 10q26.13-26.3(chr10:124988334-135427143)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 10q26.13-26.3(chr10:124988334-135427143)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated"... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 10q26.13-26.3(chr10:124988334-135427143)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 124988334,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.... | [
{
"source_db": "ClinVar",
"source_id": "ABRAXAS2",
"text": "GRCh37/hg19 10q26.13-26.3(chr10:124988334-135427143)x3 VARIANT_IN_GENE ABRAXAS2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 10q26.13-26.3(chr10:124988334-135427143)x3",
"gene": "ABRAXAS2",
"mean_phylop": 2.6550000000000002,
"track": "phyloP100way"
} | 1 |
co_cons_00081 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1 (in gene CCDC116), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1 VARIANT_IN_GENE CCDC116 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 21465662,
"track": "phyloP100way",
"window": 20,
"scores": [
0.143... | [
{
"source_db": "ClinVar",
"source_id": "CCDC116",
"text": "GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1 VARIANT_IN_GENE CCDC116",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 22q11.21-11.22(chr22:21465662-22997928)x1",
"gene": "CCDC116",
"mean_phylop": 0.027,
"track": "phyloP100way"
} | 1 |
co_cons_00082 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_002878.4(RAD51D):c.302_303del (p.Glu101fs) (in gene RAD51L3-RFFL), classify the evolutionary constraint across the variant's genomic window. | NM_002878.4(RAD51D):c.302_303del (p.Glu101fs) VARIANT_IN_GENE RAD51L3-RFFL | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002878.4(RAD51D):c.302_303del (p.Glu101fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002878.4(RAD51D):c.302_303del (p.Glu101fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_002878.4(RAD51D):c.302_303del (p.Glu101fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 35107408,
"track": "phyloP100way",
"window": 20,
"scores": [
1.22041,
... | [
{
"source_db": "ClinVar",
"source_id": "RAD51L3-RFFL",
"text": "NM_002878.4(RAD51D):c.302_303del (p.Glu101fs) VARIANT_IN_GENE RAD51L3-RFFL",
"confidence": 1
}
] | {
"variant": "NM_002878.4(RAD51D):c.302_303del (p.Glu101fs)",
"gene": "RAD51L3-RFFL",
"mean_phylop": 3.224,
"track": "phyloP100way"
} | 1 |
co_cons_00083 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 1q25.1-25.3(chr1:173138799-185129406)x3 (in gene ABL2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 1q25.1-25.3(chr1:173138799-185129406)x3 VARIANT_IN_GENE ABL2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 1q25.1-25.3(chr1:173138799-185129406)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 1q25.1-25.3(chr1:173138799-185129406)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 1q25.1-25.3(chr1:173138799-185129406)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 173138799,
"track": "phyloP100way",
"window": 20,
"scores": [
0.27629... | [
{
"source_db": "ClinVar",
"source_id": "ABL2",
"text": "GRCh37/hg19 1q25.1-25.3(chr1:173138799-185129406)x3 VARIANT_IN_GENE ABL2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 1q25.1-25.3(chr1:173138799-185129406)x3",
"gene": "ABL2",
"mean_phylop": 0.083,
"track": "phyloP100way"
} | 1 |
co_cons_00084 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 3q13.2-13.31(chr3:112465094-115774111)x1 (in gene GAP43), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 3q13.2-13.31(chr3:112465094-115774111)x1 VARIANT_IN_GENE GAP43 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 3q13.2-13.31(chr3:112465094-115774111)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 3q13.2-13.31(chr3:112465094-115774111)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 3q13.2-13.31(chr3:112465094-115774111)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 112465094,
"track": "phyloP100way",
"window": 20,
"scores": [
0.1507... | [
{
"source_db": "ClinVar",
"source_id": "GAP43",
"text": "GRCh38/hg38 3q13.2-13.31(chr3:112465094-115774111)x1 VARIANT_IN_GENE GAP43",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 3q13.2-13.31(chr3:112465094-115774111)x1",
"gene": "GAP43",
"mean_phylop": 0.07100000000000001,
"track": "phyloP100way"
} | 1 |
co_cons_00085 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 8p23.3-11.21(chr8:158048-41600696)x3 (in gene DMTN), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 8p23.3-11.21(chr8:158048-41600696)x3 VARIANT_IN_GENE DMTN | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 8p23.3-11.21(chr8:158048-41600696)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 8p23.3-11.21(chr8:158048-41600696)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 8p23.3-11.21(chr8:158048-41600696)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 158048,
"track": "phyloP100way",
"window": 20,
"scores": [
0.153945,
... | [
{
"source_db": "ClinVar",
"source_id": "DMTN",
"text": "GRCh37/hg19 8p23.3-11.21(chr8:158048-41600696)x3 VARIANT_IN_GENE DMTN",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 8p23.3-11.21(chr8:158048-41600696)x3",
"gene": "DMTN",
"mean_phylop": 0.114,
"track": "phyloP100way"
} | 1 |
co_cons_00086 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000455.5(STK11):c.1020C>G (p.Tyr340Ter) (in gene LOC130062899), classify the evolutionary constraint across the variant's genomic window. | NM_000455.5(STK11):c.1020C>G (p.Tyr340Ter) VARIANT_IN_GENE LOC130062899 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.1020C>G (p.Tyr340Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.1020C>G (p.Tyr340Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000455.5(STK11):c.1020C>G (p.Tyr340Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr19",
"pos": 1223084,
"track": "phyloP100way",
"window": 20,
"scores": [
5.92309,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC130062899",
"text": "NM_000455.5(STK11):c.1020C>G (p.Tyr340Ter) VARIANT_IN_GENE LOC130062899",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.1020C>G (p.Tyr340Ter)",
"gene": "LOC130062899",
"mean_phylop": 4.921,
"track": "phyloP100way"
} | 1 |
co_cons_00087 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000546.6(TP53):c.556del (p.Asp186fs) (in gene TP53), classify the evolutionary constraint across the variant's genomic window. | NM_000546.6(TP53):c.556del (p.Asp186fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.556del (p.Asp186fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.556del (p.Asp186fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000546.6(TP53):c.556del (p.Asp186fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 7675056,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.562197,
-... | [
{
"source_db": "ClinVar",
"source_id": "TP53",
"text": "NM_000546.6(TP53):c.556del (p.Asp186fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.556del (p.Asp186fs)",
"gene": "TP53",
"mean_phylop": 1.117,
"track": "phyloP100way"
} | 1 |
co_cons_00088 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001903.5(CTNNA1):c.1390-2A>G (in gene CTNNA1), classify the evolutionary constraint across the variant's genomic window. | NM_001903.5(CTNNA1):c.1390-2A>G VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.1390-2A>G",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.1390-2A>G",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_sour... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001903.5(CTNNA1):c.1390-2A>G",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 138917740,
"track": "phyloP100way",
"window": 20,
"scores": [
0.542252,
1.13324,
... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.1390-2A>G VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.1390-2A>G",
"gene": "CTNNA1",
"mean_phylop": 3.431,
"track": "phyloP100way"
} | 1 |
co_cons_00089 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_007294.4(BRCA1):c.3761_3770del (p.Lys1254fs) (in gene LOC126862571), classify the evolutionary constraint across the variant's genomic window. | NM_007294.4(BRCA1):c.3761_3770del (p.Lys1254fs) VARIANT_IN_GENE LOC126862571 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.3761_3770del (p.Lys1254fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.3761_3770del (p.Lys1254fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_007294.4(BRCA1):c.3761_3770del (p.Lys1254fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 43091761,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0938976,... | [
{
"source_db": "ClinVar",
"source_id": "LOC126862571",
"text": "NM_007294.4(BRCA1):c.3761_3770del (p.Lys1254fs) VARIANT_IN_GENE LOC126862571",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.3761_3770del (p.Lys1254fs)",
"gene": "LOC126862571",
"mean_phylop": 0.076,
"track": "phyloP100way"
} | 1 |
co_cons_00090 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1 (in gene ABL2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1 VARIANT_IN_GENE ABL2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 177551193,
"track": "phyloP100way",
"window": 20,
"scores": [
0.17854... | [
{
"source_db": "ClinVar",
"source_id": "ABL2",
"text": "GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1 VARIANT_IN_GENE ABL2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 1q25.2-32.1(chr1:177551193-199599056)x1",
"gene": "ABL2",
"mean_phylop": -0.002,
"track": "phyloP100way"
} | 1 |
co_cons_00091 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 17p13.1(chr17:7478195-8435524)x1 (in gene ALOX12B), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 17p13.1(chr17:7478195-8435524)x1 VARIANT_IN_GENE ALOX12B | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 17p13.1(chr17:7478195-8435524)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 17p13.1(chr17:7478195-8435524)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 17p13.1(chr17:7478195-8435524)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 7478195,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.00933858,
... | [
{
"source_db": "ClinVar",
"source_id": "ALOX12B",
"text": "GRCh38/hg38 17p13.1(chr17:7478195-8435524)x1 VARIANT_IN_GENE ALOX12B",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 17p13.1(chr17:7478195-8435524)x1",
"gene": "ALOX12B",
"mean_phylop": 1.434,
"track": "phyloP100way"
} | 1 |
co_cons_00092 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3 (in gene ABCA4), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3 VARIANT_IN_GENE ABCA4 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 93837992,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.164819... | [
{
"source_db": "ClinVar",
"source_id": "ABCA4",
"text": "GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3 VARIANT_IN_GENE ABCA4",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3",
"gene": "ABCA4",
"mean_phylop": 0.187,
"track": "phyloP100way"
} | 1 |
co_cons_00093 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 16p13.3(chr16:1505184-4415346)x3 (in gene ABCA3), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 16p13.3(chr16:1505184-4415346)x3 VARIANT_IN_GENE ABCA3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 16p13.3(chr16:1505184-4415346)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 16p13.3(chr16:1505184-4415346)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 16p13.3(chr16:1505184-4415346)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 1505184,
"track": "phyloP100way",
"window": 20,
"scores": [
1.6362,
... | [
{
"source_db": "ClinVar",
"source_id": "ABCA3",
"text": "GRCh37/hg19 16p13.3(chr16:1505184-4415346)x3 VARIANT_IN_GENE ABCA3",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 16p13.3(chr16:1505184-4415346)x3",
"gene": "ABCA3",
"mean_phylop": -0.518,
"track": "phyloP100way"
} | 1 |
co_cons_00094 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1 (in gene ACSL1), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1 VARIANT_IN_GENE ACSL1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 173854560,
"track": "phyloP100way",
"window": 20,
"scores": [
1.42956... | [
{
"source_db": "ClinVar",
"source_id": "ACSL1",
"text": "GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1 VARIANT_IN_GENE ACSL1",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 4q34.1-35.2(chr4:173854560-189548183)x1",
"gene": "ACSL1",
"mean_phylop": 0.114,
"track": "phyloP100way"
} | 1 |
co_cons_00095 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_007194.4(CHEK2):c.1039del (p.Asp347fs) (in gene CHEK2), classify the evolutionary constraint across the variant's genomic window. | NM_007194.4(CHEK2):c.1039del (p.Asp347fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.1039del (p.Asp347fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.1039del (p.Asp347fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_007194.4(CHEK2):c.1039del (p.Asp347fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 28696957,
"track": "phyloP100way",
"window": 20,
"scores": [
6.26592,
... | [
{
"source_db": "ClinVar",
"source_id": "CHEK2",
"text": "NM_007194.4(CHEK2):c.1039del (p.Asp347fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.1039del (p.Asp347fs)",
"gene": "CHEK2",
"mean_phylop": 4.075,
"track": "phyloP100way"
} | 1 |
co_cons_00096 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3 (in gene AASDH), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3 VARIANT_IN_GENE AASDH | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 52866944,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.365213,... | [
{
"source_db": "ClinVar",
"source_id": "AASDH",
"text": "GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3 VARIANT_IN_GENE AASDH",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3",
"gene": "AASDH",
"mean_phylop": -0.292,
"track": "phyloP100way"
} | 1 |
co_cons_00097 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001693.4(ATP6V1B2):c.488G>A (p.Arg163Gln) (in gene ATP6V1B2), classify the evolutionary constraint across the variant's genomic window. | NM_001693.4(ATP6V1B2):c.488G>A (p.Arg163Gln) VARIANT_IN_GENE ATP6V1B2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001693.4(ATP6V1B2):c.488G>A (p.Arg163Gln)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001693.4(ATP6V1B2):c.488G>A (p.Arg163Gln)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001693.4(ATP6V1B2):c.488G>A (p.Arg163Gln)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 20211201,
"track": "phyloP100way",
"window": 20,
"scores": [
1.06888,
... | [
{
"source_db": "ClinVar",
"source_id": "ATP6V1B2",
"text": "NM_001693.4(ATP6V1B2):c.488G>A (p.Arg163Gln) VARIANT_IN_GENE ATP6V1B2",
"confidence": 1
}
] | {
"variant": "NM_001693.4(ATP6V1B2):c.488G>A (p.Arg163Gln)",
"gene": "ATP6V1B2",
"mean_phylop": 5.86,
"track": "phyloP100way"
} | 1 |
co_cons_00098 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 2p25.3-23.1(chr2:12771-30565600)x3 (in gene ABHD1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 2p25.3-23.1(chr2:12771-30565600)x3 VARIANT_IN_GENE ABHD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 2p25.3-23.1(chr2:12771-30565600)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 2p25.3-23.1(chr2:12771-30565600)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 2p25.3-23.1(chr2:12771-30565600)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 12771,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.883378,
... | [
{
"source_db": "ClinVar",
"source_id": "ABHD1",
"text": "GRCh37/hg19 2p25.3-23.1(chr2:12771-30565600)x3 VARIANT_IN_GENE ABHD1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 2p25.3-23.1(chr2:12771-30565600)x3",
"gene": "ABHD1",
"mean_phylop": -0.164,
"track": "phyloP100way"
} | 1 |
co_cons_00099 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3 (in gene PLBD1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3 VARIANT_IN_GENE PLBD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 565369,
"track": "phyloP100way",
"window": 20,
"scores": [
0.921732,
... | [
{
"source_db": "ClinVar",
"source_id": "PLBD1",
"text": "GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3 VARIANT_IN_GENE PLBD1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3",
"gene": "PLBD1",
"mean_phylop": 2.714,
"track": "phyloP100way"
} | 1 |
co_cons_00100 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001101.5(ACTB):c.353_356delinsTGAC (p.Lys118_Met119delinsMetThr) (in gene ACTB), classify the evolutionary constraint across the variant's genomic window. | NM_001101.5(ACTB):c.353_356delinsTGAC (p.Lys118_Met119delinsMetThr) VARIANT_IN_GENE ACTB | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001101.5(ACTB):c.353_356delinsTGAC (p.Lys118_Met119delinsMetThr)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001101.5(ACTB):c.353_356delinsTGAC (p.Lys118_Met119delinsMetThr)",
"edge_relation": "VARIANT_IN_GENE",
"edge... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001101.5(ACTB):c.353_356delinsTGAC (p.Lys118_Met119delinsMetThr)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 5529168,
"track": "phyloP100way",
"window": 20,
"scores": [
... | [
{
"source_db": "ClinVar",
"source_id": "ACTB",
"text": "NM_001101.5(ACTB):c.353_356delinsTGAC (p.Lys118_Met119delinsMetThr) VARIANT_IN_GENE ACTB",
"confidence": 1
}
] | {
"variant": "NM_001101.5(ACTB):c.353_356delinsTGAC (p.Lys118_Met119delinsMetThr)",
"gene": "ACTB",
"mean_phylop": 4.675,
"track": "phyloP100way"
} | 1 |
co_cons_00101 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 8p23.1-21.1(chr8:12490999-28150620)x1 (in gene ADAMDEC1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 8p23.1-21.1(chr8:12490999-28150620)x1 VARIANT_IN_GENE ADAMDEC1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 8p23.1-21.1(chr8:12490999-28150620)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 8p23.1-21.1(chr8:12490999-28150620)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 8p23.1-21.1(chr8:12490999-28150620)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 12490999,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0443543,... | [
{
"source_db": "ClinVar",
"source_id": "ADAMDEC1",
"text": "GRCh37/hg19 8p23.1-21.1(chr8:12490999-28150620)x1 VARIANT_IN_GENE ADAMDEC1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 8p23.1-21.1(chr8:12490999-28150620)x1",
"gene": "ADAMDEC1",
"mean_phylop": -0.17200000000000001,
"track": "phyloP100way"
} | 1 |
co_cons_00102 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu) (in gene BRAF), classify the evolutionary constraint across the variant's genomic window. | NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu) VARIANT_IN_GENE BRAF | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 140781617,
"track": "phyloP100way",
"window": 20,
"scores": [
7.7907,
-... | [
{
"source_db": "ClinVar",
"source_id": "BRAF",
"text": "NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu) VARIANT_IN_GENE BRAF",
"confidence": 1
}
] | {
"variant": "NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu)",
"gene": "BRAF",
"mean_phylop": 5.383,
"track": "phyloP100way"
} | 1 |
co_cons_00103 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_014845.6(FIG4):c.1949-533A>G (in gene FIG4), classify the evolutionary constraint across the variant's genomic window. | NM_014845.6(FIG4):c.1949-533A>G VARIANT_IN_GENE FIG4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_014845.6(FIG4):c.1949-533A>G",
"source_node_type": "VARIANT",
"source_node_label": "NM_014845.6(FIG4):c.1949-533A>G",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_sour... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_014845.6(FIG4):c.1949-533A>G",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 109785769,
"track": "phyloP100way",
"window": 20,
"scores": [
0.6744800000000001,
... | [
{
"source_db": "ClinVar",
"source_id": "FIG4",
"text": "NM_014845.6(FIG4):c.1949-533A>G VARIANT_IN_GENE FIG4",
"confidence": 1
}
] | {
"variant": "NM_014845.6(FIG4):c.1949-533A>G",
"gene": "FIG4",
"mean_phylop": 0.196,
"track": "phyloP100way"
} | 1 |
co_cons_00104 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 7q21.11-21.3(chr7:77821356-93340137) (in gene DMTF1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 7q21.11-21.3(chr7:77821356-93340137) VARIANT_IN_GENE DMTF1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 7q21.11-21.3(chr7:77821356-93340137)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 7q21.11-21.3(chr7:77821356-93340137)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 7q21.11-21.3(chr7:77821356-93340137)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 77821356,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0683228,
... | [
{
"source_db": "ClinVar",
"source_id": "DMTF1",
"text": "GRCh37/hg19 7q21.11-21.3(chr7:77821356-93340137) VARIANT_IN_GENE DMTF1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 7q21.11-21.3(chr7:77821356-93340137)",
"gene": "DMTF1",
"mean_phylop": 0.068,
"track": "phyloP100way"
} | 1 |
co_cons_00105 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_006231.4(POLE):c.1033C>T (p.Gln345Ter) (in gene POLE), classify the evolutionary constraint across the variant's genomic window. | NM_006231.4(POLE):c.1033C>T (p.Gln345Ter) VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.1033C>T (p.Gln345Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.1033C>T (p.Gln345Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_006231.4(POLE):c.1033C>T (p.Gln345Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 132675808,
"track": "phyloP100way",
"window": 20,
"scores": [
0.88837000000000... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.1033C>T (p.Gln345Ter) VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.1033C>T (p.Gln345Ter)",
"gene": "POLE",
"mean_phylop": 4.122,
"track": "phyloP100way"
} | 1 |
co_cons_00106 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_003014.4(SFRP4):c.617del (p.Val206fs) (in gene SFRP4), classify the evolutionary constraint across the variant's genomic window. | NM_003014.4(SFRP4):c.617del (p.Val206fs) VARIANT_IN_GENE SFRP4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_003014.4(SFRP4):c.617del (p.Val206fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_003014.4(SFRP4):c.617del (p.Val206fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_003014.4(SFRP4):c.617del (p.Val206fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 37912293,
"track": "phyloP100way",
"window": 20,
"scores": [
5.73735,
1.... | [
{
"source_db": "ClinVar",
"source_id": "SFRP4",
"text": "NM_003014.4(SFRP4):c.617del (p.Val206fs) VARIANT_IN_GENE SFRP4",
"confidence": 1
}
] | {
"variant": "NM_003014.4(SFRP4):c.617del (p.Val206fs)",
"gene": "SFRP4",
"mean_phylop": 3.223,
"track": "phyloP100way"
} | 1 |
co_cons_00107 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000044.6(AR):c.1605del (p.Pro534_Tyr535insTer) (in gene AR), classify the evolutionary constraint across the variant's genomic window. | NM_000044.6(AR):c.1605del (p.Pro534_Tyr535insTer) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.1605del (p.Pro534_Tyr535insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.1605del (p.Pro534_Tyr535insTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000044.6(AR):c.1605del (p.Pro534_Tyr535insTer)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 67546751,
"track": "phyloP100way",
"window": 20,
"scores": [
6.275,
... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.1605del (p.Pro534_Tyr535insTer) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.1605del (p.Pro534_Tyr535insTer)",
"gene": "AR",
"mean_phylop": 2.832,
"track": "phyloP100way"
} | 1 |
co_cons_00108 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3 (in gene AARD), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3 VARIANT_IN_GENE AARD | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 113580402,
"track": "phyloP100way",
"window": 20,
"scores": [
-2.8329... | [
{
"source_db": "ClinVar",
"source_id": "AARD",
"text": "GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3 VARIANT_IN_GENE AARD",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 8q23.3-24.3(chr8:113580402-145054634)x3",
"gene": "AARD",
"mean_phylop": 0.031,
"track": "phyloP100way"
} | 1 |
co_cons_00109 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_006158.5(NEFL):c.18C>G (p.Tyr6Ter) (in gene NEFL), classify the evolutionary constraint across the variant's genomic window. | NM_006158.5(NEFL):c.18C>G (p.Tyr6Ter) VARIANT_IN_GENE NEFL | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006158.5(NEFL):c.18C>G (p.Tyr6Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006158.5(NEFL):c.18C>G (p.Tyr6Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_006158.5(NEFL):c.18C>G (p.Tyr6Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 24956498,
"track": "phyloP100way",
"window": 20,
"scores": [
3.97263,
1.200... | [
{
"source_db": "ClinVar",
"source_id": "NEFL",
"text": "NM_006158.5(NEFL):c.18C>G (p.Tyr6Ter) VARIANT_IN_GENE NEFL",
"confidence": 1
}
] | {
"variant": "NM_006158.5(NEFL):c.18C>G (p.Tyr6Ter)",
"gene": "NEFL",
"mean_phylop": 2.574,
"track": "phyloP100way"
} | 1 |
co_cons_00110 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 5q35.2-35.3(chr5:176385815-178410738)x1 (in gene B4GALT7), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 5q35.2-35.3(chr5:176385815-178410738)x1 VARIANT_IN_GENE B4GALT7 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 5q35.2-35.3(chr5:176385815-178410738)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 5q35.2-35.3(chr5:176385815-178410738)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 5q35.2-35.3(chr5:176385815-178410738)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 176385815,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0919... | [
{
"source_db": "ClinVar",
"source_id": "B4GALT7",
"text": "GRCh37/hg19 5q35.2-35.3(chr5:176385815-178410738)x1 VARIANT_IN_GENE B4GALT7",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 5q35.2-35.3(chr5:176385815-178410738)x1",
"gene": "B4GALT7",
"mean_phylop": -0.298,
"track": "phyloP100way"
} | 1 |
co_cons_00111 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000789.4(ACE):c.1361del (p.Leu454fs) (in gene ACE), classify the evolutionary constraint across the variant's genomic window. | NM_000789.4(ACE):c.1361del (p.Leu454fs) VARIANT_IN_GENE ACE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000789.4(ACE):c.1361del (p.Leu454fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000789.4(ACE):c.1361del (p.Leu454fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000789.4(ACE):c.1361del (p.Leu454fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 63483046,
"track": "phyloP100way",
"window": 20,
"scores": [
5.75009,
9.... | [
{
"source_db": "ClinVar",
"source_id": "ACE",
"text": "NM_000789.4(ACE):c.1361del (p.Leu454fs) VARIANT_IN_GENE ACE",
"confidence": 1
}
] | {
"variant": "NM_000789.4(ACE):c.1361del (p.Leu454fs)",
"gene": "ACE",
"mean_phylop": 5.365,
"track": "phyloP100way"
} | 1 |
co_cons_00112 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004119.3(FLT3):c.1773_1793dup (p.Tyr597_Glu598insAspValAspPheArgGluTyr) (in gene FLT3), classify the evolutionary constraint across the variant's genomic window. | NM_004119.3(FLT3):c.1773_1793dup (p.Tyr597_Glu598insAspValAspPheArgGluTyr) VARIANT_IN_GENE FLT3 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004119.3(FLT3):c.1773_1793dup (p.Tyr597_Glu598insAspValAspPheArgGluTyr)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004119.3(FLT3):c.1773_1793dup (p.Tyr597_Glu598insAspValAspPheArgGluTyr)",
"edge_relation": "VARIANT_IN_GENE... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004119.3(FLT3):c.1773_1793dup (p.Tyr597_Glu598insAspValAspPheArgGluTyr)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr13",
"pos": 28034125,
"track": "phyloP100way",
"window": 20,
"sco... | [
{
"source_db": "ClinVar",
"source_id": "FLT3",
"text": "NM_004119.3(FLT3):c.1773_1793dup (p.Tyr597_Glu598insAspValAspPheArgGluTyr) VARIANT_IN_GENE FLT3",
"confidence": 1
}
] | {
"variant": "NM_004119.3(FLT3):c.1773_1793dup (p.Tyr597_Glu598insAspValAspPheArgGluTyr)",
"gene": "FLT3",
"mean_phylop": 4.209,
"track": "phyloP100way"
} | 1 |
co_cons_00113 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000055.4(BCHE):c.687del (p.Ala230fs) (in gene BCHE), classify the evolutionary constraint across the variant's genomic window. | NM_000055.4(BCHE):c.687del (p.Ala230fs) VARIANT_IN_GENE BCHE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000055.4(BCHE):c.687del (p.Ala230fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000055.4(BCHE):c.687del (p.Ala230fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000055.4(BCHE):c.687del (p.Ala230fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 165830347,
"track": "phyloP100way",
"window": 20,
"scores": [
7.16233,
-0... | [
{
"source_db": "ClinVar",
"source_id": "BCHE",
"text": "NM_000055.4(BCHE):c.687del (p.Ala230fs) VARIANT_IN_GENE BCHE",
"confidence": 1
}
] | {
"variant": "NM_000055.4(BCHE):c.687del (p.Ala230fs)",
"gene": "BCHE",
"mean_phylop": 3.79,
"track": "phyloP100way"
} | 1 |
co_cons_00114 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_017617.5(NOTCH1):c.3656_3666del (p.Glu1219fs) (in gene NOTCH1), classify the evolutionary constraint across the variant's genomic window. | NM_017617.5(NOTCH1):c.3656_3666del (p.Glu1219fs) VARIANT_IN_GENE NOTCH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_017617.5(NOTCH1):c.3656_3666del (p.Glu1219fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_017617.5(NOTCH1):c.3656_3666del (p.Glu1219fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_017617.5(NOTCH1):c.3656_3666del (p.Glu1219fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 136506951,
"track": "phyloP100way",
"window": 20,
"scores": [
0.553937,
... | [
{
"source_db": "ClinVar",
"source_id": "NOTCH1",
"text": "NM_017617.5(NOTCH1):c.3656_3666del (p.Glu1219fs) VARIANT_IN_GENE NOTCH1",
"confidence": 1
}
] | {
"variant": "NM_017617.5(NOTCH1):c.3656_3666del (p.Glu1219fs)",
"gene": "NOTCH1",
"mean_phylop": 4.136,
"track": "phyloP100way"
} | 1 |
co_cons_00115 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 6q26-27(chr6:162865436-170901287)x3 (in gene DACT2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 6q26-27(chr6:162865436-170901287)x3 VARIANT_IN_GENE DACT2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 6q26-27(chr6:162865436-170901287)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 6q26-27(chr6:162865436-170901287)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 6q26-27(chr6:162865436-170901287)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 162865436,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.04313000... | [
{
"source_db": "ClinVar",
"source_id": "DACT2",
"text": "GRCh37/hg19 6q26-27(chr6:162865436-170901287)x3 VARIANT_IN_GENE DACT2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 6q26-27(chr6:162865436-170901287)x3",
"gene": "DACT2",
"mean_phylop": 0.061,
"track": "phyloP100way"
} | 1 |
co_cons_00116 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 5q32-35.3(chr5:149010383-180719789) (in gene HK3), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 5q32-35.3(chr5:149010383-180719789) VARIANT_IN_GENE HK3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 5q32-35.3(chr5:149010383-180719789)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 5q32-35.3(chr5:149010383-180719789)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 5q32-35.3(chr5:149010383-180719789)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 149010383,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.764157,
... | [
{
"source_db": "ClinVar",
"source_id": "HK3",
"text": "GRCh37/hg19 5q32-35.3(chr5:149010383-180719789) VARIANT_IN_GENE HK3",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 5q32-35.3(chr5:149010383-180719789)",
"gene": "HK3",
"mean_phylop": 2.645,
"track": "phyloP100way"
} | 1 |
co_cons_00117 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 1q42.2-44(chr1:233012994-249206918)x1 (in gene ACTN2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 1q42.2-44(chr1:233012994-249206918)x1 VARIANT_IN_GENE ACTN2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 1q42.2-44(chr1:233012994-249206918)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 1q42.2-44(chr1:233012994-249206918)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 1q42.2-44(chr1:233012994-249206918)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 233012994,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.663339... | [
{
"source_db": "ClinVar",
"source_id": "ACTN2",
"text": "GRCh37/hg19 1q42.2-44(chr1:233012994-249206918)x1 VARIANT_IN_GENE ACTN2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 1q42.2-44(chr1:233012994-249206918)x1",
"gene": "ACTN2",
"mean_phylop": -0.295,
"track": "phyloP100way"
} | 1 |
co_cons_00118 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000002.11:g.(?_71004499)_(74779761_?)del (in gene C2orf78), classify the evolutionary constraint across the variant's genomic window. | NC_000002.11:g.(?_71004499)_(74779761_?)del VARIANT_IN_GENE C2orf78 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000002.11:g.(?_71004499)_(74779761_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000002.11:g.(?_71004499)_(74779761_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000002.11:g.(?_71004499)_(74779761_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 71004499,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.523394,
... | [
{
"source_db": "ClinVar",
"source_id": "C2orf78",
"text": "NC_000002.11:g.(?_71004499)_(74779761_?)del VARIANT_IN_GENE C2orf78",
"confidence": 1
}
] | {
"variant": "NC_000002.11:g.(?_71004499)_(74779761_?)del",
"gene": "C2orf78",
"mean_phylop": -0.123,
"track": "phyloP100way"
} | 1 |
co_cons_00119 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_016222.4(DDX41):c.1603_1605delinsA (p.Phe535fs) (in gene DDX41), classify the evolutionary constraint across the variant's genomic window. | NM_016222.4(DDX41):c.1603_1605delinsA (p.Phe535fs) VARIANT_IN_GENE DDX41 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_016222.4(DDX41):c.1603_1605delinsA (p.Phe535fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_016222.4(DDX41):c.1603_1605delinsA (p.Phe535fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_016222.4(DDX41):c.1603_1605delinsA (p.Phe535fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 177512338,
"track": "phyloP100way",
"window": 20,
"scores": [
7.80128,... | [
{
"source_db": "ClinVar",
"source_id": "DDX41",
"text": "NM_016222.4(DDX41):c.1603_1605delinsA (p.Phe535fs) VARIANT_IN_GENE DDX41",
"confidence": 1
}
] | {
"variant": "NM_016222.4(DDX41):c.1603_1605delinsA (p.Phe535fs)",
"gene": "DDX41",
"mean_phylop": 5.964,
"track": "phyloP100way"
} | 1 |
co_cons_00120 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3 (in gene LOC130065447), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3 VARIANT_IN_GENE LOC130065447 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 89939,
"track": "phyloP100way",
"window": 20,
"scores": [
0.641197,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC130065447",
"text": "GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3 VARIANT_IN_GENE LOC130065447",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3",
"gene": "LOC130065447",
"mean_phylop": 0.439,
"track": "phyloP100way"
} | 1 |
co_cons_00121 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 15q26.1-26.3(chr15:90288175-102429112)x3 (in gene ADAMTS17), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 15q26.1-26.3(chr15:90288175-102429112)x3 VARIANT_IN_GENE ADAMTS17 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 15q26.1-26.3(chr15:90288175-102429112)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 15q26.1-26.3(chr15:90288175-102429112)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 15q26.1-26.3(chr15:90288175-102429112)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr15",
"pos": 90288175,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0825... | [
{
"source_db": "ClinVar",
"source_id": "ADAMTS17",
"text": "GRCh37/hg19 15q26.1-26.3(chr15:90288175-102429112)x3 VARIANT_IN_GENE ADAMTS17",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 15q26.1-26.3(chr15:90288175-102429112)x3",
"gene": "ADAMTS17",
"mean_phylop": -0.035,
"track": "phyloP100way"
} | 1 |
co_cons_00122 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_170606.3(KMT2C):c.10480_10483del (p.Asn3494fs) (in gene KMT2C), classify the evolutionary constraint across the variant's genomic window. | NM_170606.3(KMT2C):c.10480_10483del (p.Asn3494fs) VARIANT_IN_GENE KMT2C | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_170606.3(KMT2C):c.10480_10483del (p.Asn3494fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_170606.3(KMT2C):c.10480_10483del (p.Asn3494fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_170606.3(KMT2C):c.10480_10483del (p.Asn3494fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 152163094,
"track": "phyloP100way",
"window": 20,
"scores": [
0.8645349... | [
{
"source_db": "ClinVar",
"source_id": "KMT2C",
"text": "NM_170606.3(KMT2C):c.10480_10483del (p.Asn3494fs) VARIANT_IN_GENE KMT2C",
"confidence": 1
}
] | {
"variant": "NM_170606.3(KMT2C):c.10480_10483del (p.Asn3494fs)",
"gene": "KMT2C",
"mean_phylop": 2.349,
"track": "phyloP100way"
} | 1 |
co_cons_00123 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004304.5(ALK):c.3522C>G (p.Phe1174Leu) (in gene ALK), classify the evolutionary constraint across the variant's genomic window. | NM_004304.5(ALK):c.3522C>G (p.Phe1174Leu) VARIANT_IN_GENE ALK | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004304.5(ALK):c.3522C>G (p.Phe1174Leu)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004304.5(ALK):c.3522C>G (p.Phe1174Leu)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004304.5(ALK):c.3522C>G (p.Phe1174Leu)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 29220829,
"track": "phyloP100way",
"window": 20,
"scores": [
7.88176,
7... | [
{
"source_db": "ClinVar",
"source_id": "ALK",
"text": "NM_004304.5(ALK):c.3522C>G (p.Phe1174Leu) VARIANT_IN_GENE ALK",
"confidence": 1
}
] | {
"variant": "NM_004304.5(ALK):c.3522C>G (p.Phe1174Leu)",
"gene": "ALK",
"mean_phylop": 4.843,
"track": "phyloP100way"
} | 1 |
co_cons_00124 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555) (in gene HAR1A), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555) VARIANT_IN_GENE HAR1A | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 56835739,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.1156... | [
{
"source_db": "ClinVar",
"source_id": "HAR1A",
"text": "GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555) VARIANT_IN_GENE HAR1A",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555)",
"gene": "HAR1A",
"mean_phylop": -0.047,
"track": "phyloP100way"
} | 1 |
co_cons_00125 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3 (in gene TRBV7-2), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3 VARIANT_IN_GENE TRBV7-2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 132850196,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.6228... | [
{
"source_db": "ClinVar",
"source_id": "TRBV7-2",
"text": "GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3 VARIANT_IN_GENE TRBV7-2",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3",
"gene": "TRBV7-2",
"mean_phylop": 0.28200000000000003,
"track": "phyloP100way"
} | 1 |
co_cons_00126 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000157.4(GBA1):c.876del (p.Glu293fs) (in gene GBA1), classify the evolutionary constraint across the variant's genomic window. | NM_000157.4(GBA1):c.876del (p.Glu293fs) VARIANT_IN_GENE GBA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000157.4(GBA1):c.876del (p.Glu293fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000157.4(GBA1):c.876del (p.Glu293fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000157.4(GBA1):c.876del (p.Glu293fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 155237464,
"track": "phyloP100way",
"window": 20,
"scores": [
8.00448,
2.... | [
{
"source_db": "ClinVar",
"source_id": "GBA1",
"text": "NM_000157.4(GBA1):c.876del (p.Glu293fs) VARIANT_IN_GENE GBA1",
"confidence": 1
}
] | {
"variant": "NM_000157.4(GBA1):c.876del (p.Glu293fs)",
"gene": "GBA1",
"mean_phylop": 4.034,
"track": "phyloP100way"
} | 1 |
co_cons_00127 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1 (in gene AMMECR1L), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1 VARIANT_IN_GENE AMMECR1L | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 122847356,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.5695... | [
{
"source_db": "ClinVar",
"source_id": "AMMECR1L",
"text": "GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1 VARIANT_IN_GENE AMMECR1L",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 2q14.3-21.1(chr2:122847356-129545581)x1",
"gene": "AMMECR1L",
"mean_phylop": -0.135,
"track": "phyloP100way"
} | 1 |
co_cons_00128 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000157.4(GBA1):c.1319C>T (p.Pro440Leu) (in gene LOC106627981), classify the evolutionary constraint across the variant's genomic window. | NM_000157.4(GBA1):c.1319C>T (p.Pro440Leu) VARIANT_IN_GENE LOC106627981 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000157.4(GBA1):c.1319C>T (p.Pro440Leu)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000157.4(GBA1):c.1319C>T (p.Pro440Leu)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000157.4(GBA1):c.1319C>T (p.Pro440Leu)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 155235750,
"track": "phyloP100way",
"window": 20,
"scores": [
2.6474,
0... | [
{
"source_db": "ClinVar",
"source_id": "LOC106627981",
"text": "NM_000157.4(GBA1):c.1319C>T (p.Pro440Leu) VARIANT_IN_GENE LOC106627981",
"confidence": 1
}
] | {
"variant": "NM_000157.4(GBA1):c.1319C>T (p.Pro440Leu)",
"gene": "LOC106627981",
"mean_phylop": 3.637,
"track": "phyloP100way"
} | 1 |
co_cons_00129 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 21q22.11-22.3(chr21:34586759-48097372)x3 (in gene ABCG1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 21q22.11-22.3(chr21:34586759-48097372)x3 VARIANT_IN_GENE ABCG1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 21q22.11-22.3(chr21:34586759-48097372)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 21q22.11-22.3(chr21:34586759-48097372)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 21q22.11-22.3(chr21:34586759-48097372)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 34586759,
"track": "phyloP100way",
"window": 20,
"scores": [
-2.969... | [
{
"source_db": "ClinVar",
"source_id": "ABCG1",
"text": "GRCh37/hg19 21q22.11-22.3(chr21:34586759-48097372)x3 VARIANT_IN_GENE ABCG1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 21q22.11-22.3(chr21:34586759-48097372)x3",
"gene": "ABCG1",
"mean_phylop": -0.03,
"track": "phyloP100way"
} | 1 |
co_cons_00130 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1 (in gene EFHD2), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1 VARIANT_IN_GENE EFHD2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 9428538,
"track": "phyloP100way",
"window": 20,
"scores": [
0.227268,
... | [
{
"source_db": "ClinVar",
"source_id": "EFHD2",
"text": "GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1 VARIANT_IN_GENE EFHD2",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 1p36.22-36.21(chr1:9428538-15815791)x1",
"gene": "EFHD2",
"mean_phylop": -0.269,
"track": "phyloP100way"
} | 1 |
co_cons_00131 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1 (in gene AASDH), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1 VARIANT_IN_GENE AASDH | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 54198601,
"track": "phyloP100way",
"window": 20,
"scores": [
0.440409,
... | [
{
"source_db": "ClinVar",
"source_id": "AASDH",
"text": "GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1 VARIANT_IN_GENE AASDH",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 4q12-13.1(chr4:54198601-62270115)x1",
"gene": "AASDH",
"mean_phylop": 0.61,
"track": "phyloP100way"
} | 1 |
co_cons_00132 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 21q22.11-22.3(chr21:32634806-43353470)x1 (in gene ATP5PO), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 21q22.11-22.3(chr21:32634806-43353470)x1 VARIANT_IN_GENE ATP5PO | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 21q22.11-22.3(chr21:32634806-43353470)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 21q22.11-22.3(chr21:32634806-43353470)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 21q22.11-22.3(chr21:32634806-43353470)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 32634806,
"track": "phyloP100way",
"window": 20,
"scores": [
7.0087... | [
{
"source_db": "ClinVar",
"source_id": "ATP5PO",
"text": "GRCh37/hg19 21q22.11-22.3(chr21:32634806-43353470)x1 VARIANT_IN_GENE ATP5PO",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 21q22.11-22.3(chr21:32634806-43353470)x1",
"gene": "ATP5PO",
"mean_phylop": 2.226,
"track": "phyloP100way"
} | 1 |
co_cons_00133 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001040108.2(MLH3):c.549_550insG (p.Ser184fs) (in gene MLH3), classify the evolutionary constraint across the variant's genomic window. | NM_001040108.2(MLH3):c.549_550insG (p.Ser184fs) VARIANT_IN_GENE MLH3 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001040108.2(MLH3):c.549_550insG (p.Ser184fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001040108.2(MLH3):c.549_550insG (p.Ser184fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001040108.2(MLH3):c.549_550insG (p.Ser184fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 75049106,
"track": "phyloP100way",
"window": 20,
"scores": [
0.427787,
... | [
{
"source_db": "ClinVar",
"source_id": "MLH3",
"text": "NM_001040108.2(MLH3):c.549_550insG (p.Ser184fs) VARIANT_IN_GENE MLH3",
"confidence": 1
}
] | {
"variant": "NM_001040108.2(MLH3):c.549_550insG (p.Ser184fs)",
"gene": "MLH3",
"mean_phylop": 4.808,
"track": "phyloP100way"
} | 1 |
co_cons_00134 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000245.4(MET):c.3749T>C (p.Met1250Thr) (in gene MET), classify the evolutionary constraint across the variant's genomic window. | NM_000245.4(MET):c.3749T>C (p.Met1250Thr) VARIANT_IN_GENE MET | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000245.4(MET):c.3749T>C (p.Met1250Thr)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000245.4(MET):c.3749T>C (p.Met1250Thr)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000245.4(MET):c.3749T>C (p.Met1250Thr)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 116783420,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.52278,
... | [
{
"source_db": "ClinVar",
"source_id": "MET",
"text": "NM_000245.4(MET):c.3749T>C (p.Met1250Thr) VARIANT_IN_GENE MET",
"confidence": 1
}
] | {
"variant": "NM_000245.4(MET):c.3749T>C (p.Met1250Thr)",
"gene": "MET",
"mean_phylop": 5.914,
"track": "phyloP100way"
} | 1 |
co_cons_00135 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 4p16.3-15.32(chr4:68345-15973383)x1 (in gene ABLIM2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 4p16.3-15.32(chr4:68345-15973383)x1 VARIANT_IN_GENE ABLIM2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 4p16.3-15.32(chr4:68345-15973383)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 4p16.3-15.32(chr4:68345-15973383)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 4p16.3-15.32(chr4:68345-15973383)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 68345,
"track": "phyloP100way",
"window": 20,
"scores": [
0.247685,
... | [
{
"source_db": "ClinVar",
"source_id": "ABLIM2",
"text": "GRCh37/hg19 4p16.3-15.32(chr4:68345-15973383)x1 VARIANT_IN_GENE ABLIM2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 4p16.3-15.32(chr4:68345-15973383)x1",
"gene": "ABLIM2",
"mean_phylop": 0.023,
"track": "phyloP100way"
} | 1 |
co_cons_00136 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1 (in gene ADAMTS3), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1 VARIANT_IN_GENE ADAMTS3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 68950363,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.852244... | [
{
"source_db": "ClinVar",
"source_id": "ADAMTS3",
"text": "GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1 VARIANT_IN_GENE ADAMTS3",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 4q13.2-21.21(chr4:68950363-79738598)x1",
"gene": "ADAMTS3",
"mean_phylop": -0.615,
"track": "phyloP100way"
} | 1 |
co_cons_00137 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001291415.2(KDM6A):c.4161+5_4161+8del (in gene KDM6A), classify the evolutionary constraint across the variant's genomic window. | NM_001291415.2(KDM6A):c.4161+5_4161+8del VARIANT_IN_GENE KDM6A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001291415.2(KDM6A):c.4161+5_4161+8del",
"source_node_type": "VARIANT",
"source_node_label": "NM_001291415.2(KDM6A):c.4161+5_4161+8del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001291415.2(KDM6A):c.4161+5_4161+8del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 45107535,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.287063,
... | [
{
"source_db": "ClinVar",
"source_id": "KDM6A",
"text": "NM_001291415.2(KDM6A):c.4161+5_4161+8del VARIANT_IN_GENE KDM6A",
"confidence": 1
}
] | {
"variant": "NM_001291415.2(KDM6A):c.4161+5_4161+8del",
"gene": "KDM6A",
"mean_phylop": 3.642,
"track": "phyloP100way"
} | 1 |
co_cons_00138 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 8p21.2-12(chr8:24514488-34808438) (in gene ADRA1A), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 8p21.2-12(chr8:24514488-34808438) VARIANT_IN_GENE ADRA1A | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 8p21.2-12(chr8:24514488-34808438)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 8p21.2-12(chr8:24514488-34808438)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 8p21.2-12(chr8:24514488-34808438)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 24514488,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.06220469999... | [
{
"source_db": "ClinVar",
"source_id": "ADRA1A",
"text": "GRCh37/hg19 8p21.2-12(chr8:24514488-34808438) VARIANT_IN_GENE ADRA1A",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 8p21.2-12(chr8:24514488-34808438)",
"gene": "ADRA1A",
"mean_phylop": -0.016,
"track": "phyloP100way"
} | 1 |
co_cons_00139 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1 (in gene ADAM11), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1 VARIANT_IN_GENE ADAM11 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 43934167,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.23926000... | [
{
"source_db": "ClinVar",
"source_id": "ADAM11",
"text": "GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1 VARIANT_IN_GENE ADAM11",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 17q21.31(chr17:43934167-44854025)x1",
"gene": "ADAM11",
"mean_phylop": 0.015,
"track": "phyloP100way"
} | 1 |
co_cons_00140 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_022552.5(DNMT3A):c.1978T>C (p.Tyr660His) (in gene DNMT3A), classify the evolutionary constraint across the variant's genomic window. | NM_022552.5(DNMT3A):c.1978T>C (p.Tyr660His) VARIANT_IN_GENE DNMT3A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_022552.5(DNMT3A):c.1978T>C (p.Tyr660His)",
"source_node_type": "VARIANT",
"source_node_label": "NM_022552.5(DNMT3A):c.1978T>C (p.Tyr660His)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_022552.5(DNMT3A):c.1978T>C (p.Tyr660His)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 25241666,
"track": "phyloP100way",
"window": 20,
"scores": [
9.325,
6... | [
{
"source_db": "ClinVar",
"source_id": "DNMT3A",
"text": "NM_022552.5(DNMT3A):c.1978T>C (p.Tyr660His) VARIANT_IN_GENE DNMT3A",
"confidence": 1
}
] | {
"variant": "NM_022552.5(DNMT3A):c.1978T>C (p.Tyr660His)",
"gene": "DNMT3A",
"mean_phylop": 5.189,
"track": "phyloP100way"
} | 1 |
co_cons_00141 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3 (in gene CEP55), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3 VARIANT_IN_GENE CEP55 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 93297,
"track": "phyloP100way",
"window": 20,
"scores": [
0.625842999... | [
{
"source_db": "ClinVar",
"source_id": "CEP55",
"text": "GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3 VARIANT_IN_GENE CEP55",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 10p15.3-q26.3(chr10:93297-135378918)x3",
"gene": "CEP55",
"mean_phylop": 0.457,
"track": "phyloP100way"
} | 1 |
co_cons_00142 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 16p12.2-11.2(chr16:21475039-29043958)x1 (in gene APOBR), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 16p12.2-11.2(chr16:21475039-29043958)x1 VARIANT_IN_GENE APOBR | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 16p12.2-11.2(chr16:21475039-29043958)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 16p12.2-11.2(chr16:21475039-29043958)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 16p12.2-11.2(chr16:21475039-29043958)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 21467726,
"track": "phyloP100way",
"window": 20,
"scores": [
0.89636... | [
{
"source_db": "ClinVar",
"source_id": "APOBR",
"text": "GRCh37/hg19 16p12.2-11.2(chr16:21475039-29043958)x1 VARIANT_IN_GENE APOBR",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 16p12.2-11.2(chr16:21475039-29043958)x1",
"gene": "APOBR",
"mean_phylop": 0.018000000000000002,
"track": "phyloP100way"
} | 1 |
co_cons_00143 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001291303.3(FAT4):c.1195del (p.Leu399fs) (in gene FAT4), classify the evolutionary constraint across the variant's genomic window. | NM_001291303.3(FAT4):c.1195del (p.Leu399fs) VARIANT_IN_GENE FAT4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001291303.3(FAT4):c.1195del (p.Leu399fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001291303.3(FAT4):c.1195del (p.Leu399fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001291303.3(FAT4):c.1195del (p.Leu399fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 125317606,
"track": "phyloP100way",
"window": 20,
"scores": [
9.66998,
... | [
{
"source_db": "ClinVar",
"source_id": "FAT4",
"text": "NM_001291303.3(FAT4):c.1195del (p.Leu399fs) VARIANT_IN_GENE FAT4",
"confidence": 1
}
] | {
"variant": "NM_001291303.3(FAT4):c.1195del (p.Leu399fs)",
"gene": "FAT4",
"mean_phylop": 4.714,
"track": "phyloP100way"
} | 1 |
co_cons_00144 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3 (in gene LINC02247), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3 VARIANT_IN_GENE LINC02247 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 132986903,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0539... | [
{
"source_db": "ClinVar",
"source_id": "LINC02247",
"text": "GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3 VARIANT_IN_GENE LINC02247",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3",
"gene": "LINC02247",
"mean_phylop": -0.491,
"track": "phyloP100way"
} | 1 |
co_cons_00145 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_198578.4(LRRK2):c.4322G>A (p.Arg1441His) (in gene LRRK2), classify the evolutionary constraint across the variant's genomic window. | NM_198578.4(LRRK2):c.4322G>A (p.Arg1441His) VARIANT_IN_GENE LRRK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_198578.4(LRRK2):c.4322G>A (p.Arg1441His)",
"source_node_type": "VARIANT",
"source_node_label": "NM_198578.4(LRRK2):c.4322G>A (p.Arg1441His)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_198578.4(LRRK2):c.4322G>A (p.Arg1441His)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 40310435,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.375772,
... | [
{
"source_db": "ClinVar",
"source_id": "LRRK2",
"text": "NM_198578.4(LRRK2):c.4322G>A (p.Arg1441His) VARIANT_IN_GENE LRRK2",
"confidence": 1
}
] | {
"variant": "NM_198578.4(LRRK2):c.4322G>A (p.Arg1441His)",
"gene": "LRRK2",
"mean_phylop": 2.699,
"track": "phyloP100way"
} | 1 |
co_cons_00146 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_015338.6(ASXL1):c.3677_3678del (p.Leu1226fs) (in gene ASXL1), classify the evolutionary constraint across the variant's genomic window. | NM_015338.6(ASXL1):c.3677_3678del (p.Leu1226fs) VARIANT_IN_GENE ASXL1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_015338.6(ASXL1):c.3677_3678del (p.Leu1226fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_015338.6(ASXL1):c.3677_3678del (p.Leu1226fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_015338.6(ASXL1):c.3677_3678del (p.Leu1226fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 32436389,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.44508699... | [
{
"source_db": "ClinVar",
"source_id": "ASXL1",
"text": "NM_015338.6(ASXL1):c.3677_3678del (p.Leu1226fs) VARIANT_IN_GENE ASXL1",
"confidence": 1
}
] | {
"variant": "NM_015338.6(ASXL1):c.3677_3678del (p.Leu1226fs)",
"gene": "ASXL1",
"mean_phylop": 1.441,
"track": "phyloP100way"
} | 1 |
co_cons_00147 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 10q26.13-26.3(chr10:126914469-135427143)x1 (in gene ADAM12), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 10q26.13-26.3(chr10:126914469-135427143)x1 VARIANT_IN_GENE ADAM12 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 10q26.13-26.3(chr10:126914469-135427143)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 10q26.13-26.3(chr10:126914469-135427143)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated"... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 10q26.13-26.3(chr10:126914469-135427143)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 126914469,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.... | [
{
"source_db": "ClinVar",
"source_id": "ADAM12",
"text": "GRCh37/hg19 10q26.13-26.3(chr10:126914469-135427143)x1 VARIANT_IN_GENE ADAM12",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 10q26.13-26.3(chr10:126914469-135427143)x1",
"gene": "ADAM12",
"mean_phylop": -0.167,
"track": "phyloP100way"
} | 1 |
co_cons_00148 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 22q11.22-11.23(chr22:22962196-25059631)x3 (in gene ADORA2A), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 22q11.22-11.23(chr22:22962196-25059631)x3 VARIANT_IN_GENE ADORA2A | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 22q11.22-11.23(chr22:22962196-25059631)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 22q11.22-11.23(chr22:22962196-25059631)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 22q11.22-11.23(chr22:22962196-25059631)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 22962196,
"track": "phyloP100way",
"window": 20,
"scores": [
0.339... | [
{
"source_db": "ClinVar",
"source_id": "ADORA2A",
"text": "GRCh37/hg19 22q11.22-11.23(chr22:22962196-25059631)x3 VARIANT_IN_GENE ADORA2A",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 22q11.22-11.23(chr22:22962196-25059631)x3",
"gene": "ADORA2A",
"mean_phylop": 0.001,
"track": "phyloP100way"
} | 1 |
co_cons_00149 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_032409.3(PINK1):c.1570_1573dup (p.Asp525fs) (in gene PINK1), classify the evolutionary constraint across the variant's genomic window. | NM_032409.3(PINK1):c.1570_1573dup (p.Asp525fs) VARIANT_IN_GENE PINK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032409.3(PINK1):c.1570_1573dup (p.Asp525fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032409.3(PINK1):c.1570_1573dup (p.Asp525fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_032409.3(PINK1):c.1570_1573dup (p.Asp525fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 20650512,
"track": "phyloP100way",
"window": 20,
"scores": [
1.96127,
... | [
{
"source_db": "ClinVar",
"source_id": "PINK1",
"text": "NM_032409.3(PINK1):c.1570_1573dup (p.Asp525fs) VARIANT_IN_GENE PINK1",
"confidence": 1
}
] | {
"variant": "NM_032409.3(PINK1):c.1570_1573dup (p.Asp525fs)",
"gene": "PINK1",
"mean_phylop": 1.929,
"track": "phyloP100way"
} | 1 |
co_cons_00150 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 1q25.2-31.3(chr1:176595962-196301688)x1 (in gene ABL2), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 1q25.2-31.3(chr1:176595962-196301688)x1 VARIANT_IN_GENE ABL2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 1q25.2-31.3(chr1:176595962-196301688)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 1q25.2-31.3(chr1:176595962-196301688)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 1q25.2-31.3(chr1:176595962-196301688)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 176595962,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.6078... | [
{
"source_db": "ClinVar",
"source_id": "ABL2",
"text": "GRCh38/hg38 1q25.2-31.3(chr1:176595962-196301688)x1 VARIANT_IN_GENE ABL2",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 1q25.2-31.3(chr1:176595962-196301688)x1",
"gene": "ABL2",
"mean_phylop": -0.425,
"track": "phyloP100way"
} | 1 |
co_cons_00151 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000789.4(ACE):c.2062C>T (p.Gln688Ter) (in gene ACE), classify the evolutionary constraint across the variant's genomic window. | NM_000789.4(ACE):c.2062C>T (p.Gln688Ter) VARIANT_IN_GENE ACE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 63486560,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.06983,
... | [
{
"source_db": "ClinVar",
"source_id": "ACE",
"text": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter) VARIANT_IN_GENE ACE",
"confidence": 1
}
] | {
"variant": "NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)",
"gene": "ACE",
"mean_phylop": 1.654,
"track": "phyloP100way"
} | 1 |
co_cons_00152 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 (in gene LOC107986118), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 VARIANT_IN_GENE LOC107986118 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 93886671,
"track": "phyloP100way",
"window": 20,
"scores": [
0.241724,... | [
{
"source_db": "ClinVar",
"source_id": "LOC107986118",
"text": "GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 VARIANT_IN_GENE LOC107986118",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1",
"gene": "LOC107986118",
"mean_phylop": 0.47900000000000004,
"track": "phyloP100way"
} | 1 |
co_cons_00153 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000038.6(APC):c.2478del(p.Asn827fs) (in gene APC), classify the evolutionary constraint across the variant's genomic window. | NM_000038.6(APC):c.2478del(p.Asn827fs) VARIANT_HAS_VEP_CONSEQUENCE APC | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000038.6(APC):c.2478del(p.Asn827fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000038.6(APC):c.2478del(p.Asn827fs)",
"edge_relation": "VARIANT_HAS_VEP_CONSEQUENCE",
"edge_evidence_type": "computational_prediction",
... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"snp_sequence"
] | [
{
"family": "sequence",
"tag": "snp_sequence",
"anchor_node_id": "NM_000038.6(APC):c.2478del(p.Asn827fs)",
"source_db": "Ensembl",
"payload": {
"chrom": "5",
"pos": 112838072,
"ref_allele": "G",
"alt_allele": "-",
"ref_context": "AGGTCAGACAATTTTAATACTGGCAACATGACTGTC... | [
{
"source_db": "Ensembl_VEP",
"source_id": "APC",
"text": "NM_000038.6(APC):c.2478del(p.Asn827fs) VARIANT_HAS_VEP_CONSEQUENCE APC",
"confidence": 0.95
}
] | {
"variant": "NM_000038.6(APC):c.2478del(p.Asn827fs)",
"gene": "APC",
"mean_phylop": 3.508,
"track": "phyloP100way"
} | 0.95 |
co_cons_00154 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 (in gene FAM83H), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 VARIANT_IN_GENE FAM83H | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 124514090,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.067... | [
{
"source_db": "ClinVar",
"source_id": "FAM83H",
"text": "GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 VARIANT_IN_GENE FAM83H",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3",
"gene": "FAM83H",
"mean_phylop": -0.096,
"track": "phyloP100way"
} | 1 |
co_cons_00155 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1 (in gene PRR18), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1 VARIANT_IN_GENE PRR18 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 160484810,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.512764... | [
{
"source_db": "ClinVar",
"source_id": "PRR18",
"text": "GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1 VARIANT_IN_GENE PRR18",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1",
"gene": "PRR18",
"mean_phylop": -0.619,
"track": "phyloP100way"
} | 1 |
co_cons_00156 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001626.6(AKT2):c.821G>A (p.Arg274His) (in gene AKT2), classify the evolutionary constraint across the variant's genomic window. | NM_001626.6(AKT2):c.821G>A (p.Arg274His) VARIANT_IN_GENE AKT2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001626.6(AKT2):c.821G>A (p.Arg274His)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001626.6(AKT2):c.821G>A (p.Arg274His)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001626.6(AKT2):c.821G>A (p.Arg274His)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr19",
"pos": 40237979,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.55361,
... | [
{
"source_db": "ClinVar",
"source_id": "AKT2",
"text": "NM_001626.6(AKT2):c.821G>A (p.Arg274His) VARIANT_IN_GENE AKT2",
"confidence": 1
}
] | {
"variant": "NM_001626.6(AKT2):c.821G>A (p.Arg274His)",
"gene": "AKT2",
"mean_phylop": 3.536,
"track": "phyloP100way"
} | 1 |
co_cons_00157 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_013254.4(TBK1):c.1638_1641del (p.Asp546fs) (in gene TBK1), classify the evolutionary constraint across the variant's genomic window. | NM_013254.4(TBK1):c.1638_1641del (p.Asp546fs) VARIANT_IN_GENE TBK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_013254.4(TBK1):c.1638_1641del (p.Asp546fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_013254.4(TBK1):c.1638_1641del (p.Asp546fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_013254.4(TBK1):c.1638_1641del (p.Asp546fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 64495596,
"track": "phyloP100way",
"window": 20,
"scores": [
4.50127,
... | [
{
"source_db": "ClinVar",
"source_id": "TBK1",
"text": "NM_013254.4(TBK1):c.1638_1641del (p.Asp546fs) VARIANT_IN_GENE TBK1",
"confidence": 1
}
] | {
"variant": "NM_013254.4(TBK1):c.1638_1641del (p.Asp546fs)",
"gene": "TBK1",
"mean_phylop": 3.605,
"track": "phyloP100way"
} | 1 |
co_cons_00158 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000789.4(ACE):c.793C>T (p.Arg265Ter) (in gene ACE), classify the evolutionary constraint across the variant's genomic window. | NM_000789.4(ACE):c.793C>T (p.Arg265Ter) VARIANT_IN_GENE ACE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 63480474,
"track": "phyloP100way",
"window": 20,
"scores": [
7.97424,
0.... | [
{
"source_db": "ClinVar",
"source_id": "ACE",
"text": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter) VARIANT_IN_GENE ACE",
"confidence": 1
}
] | {
"variant": "NM_000789.4(ACE):c.793C>T (p.Arg265Ter)",
"gene": "ACE",
"mean_phylop": 3.431,
"track": "phyloP100way"
} | 1 |
co_cons_00159 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_016222.4(DDX41):c.758C>G (p.Ser253Ter) (in gene DDX41), classify the evolutionary constraint across the variant's genomic window. | NM_016222.4(DDX41):c.758C>G (p.Ser253Ter) VARIANT_IN_GENE DDX41 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_016222.4(DDX41):c.758C>G (p.Ser253Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_016222.4(DDX41):c.758C>G (p.Ser253Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_016222.4(DDX41):c.758C>G (p.Ser253Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 177514956,
"track": "phyloP100way",
"window": 20,
"scores": [
7.31243,
... | [
{
"source_db": "ClinVar",
"source_id": "DDX41",
"text": "NM_016222.4(DDX41):c.758C>G (p.Ser253Ter) VARIANT_IN_GENE DDX41",
"confidence": 1
}
] | {
"variant": "NM_016222.4(DDX41):c.758C>G (p.Ser253Ter)",
"gene": "DDX41",
"mean_phylop": 4.766,
"track": "phyloP100way"
} | 1 |
co_cons_00160 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004738.5(VAPB):c.137C>T (p.Thr46Ile) (in gene VAPB), classify the evolutionary constraint across the variant's genomic window. | NM_004738.5(VAPB):c.137C>T (p.Thr46Ile) VARIANT_IN_GENE VAPB | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004738.5(VAPB):c.137C>T (p.Thr46Ile)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004738.5(VAPB):c.137C>T (p.Thr46Ile)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004738.5(VAPB):c.137C>T (p.Thr46Ile)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 58418289,
"track": "phyloP100way",
"window": 20,
"scores": [
0.715496,
8... | [
{
"source_db": "ClinVar",
"source_id": "VAPB",
"text": "NM_004738.5(VAPB):c.137C>T (p.Thr46Ile) VARIANT_IN_GENE VAPB",
"confidence": 1
}
] | {
"variant": "NM_004738.5(VAPB):c.137C>T (p.Thr46Ile)",
"gene": "VAPB",
"mean_phylop": 5.612,
"track": "phyloP100way"
} | 1 |
co_cons_00161 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 17q21.31(chr17:45637714-46118962)x1 (in gene CRHR1), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 17q21.31(chr17:45637714-46118962)x1 VARIANT_IN_GENE CRHR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 17q21.31(chr17:45637714-46118962)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 17q21.31(chr17:45637714-46118962)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 17q21.31(chr17:45637714-46118962)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 45637714,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.03615749... | [
{
"source_db": "ClinVar",
"source_id": "CRHR1",
"text": "GRCh38/hg38 17q21.31(chr17:45637714-46118962)x1 VARIANT_IN_GENE CRHR1",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 17q21.31(chr17:45637714-46118962)x1",
"gene": "CRHR1",
"mean_phylop": 0.627,
"track": "phyloP100way"
} | 1 |
co_cons_00162 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1 (in gene ZBTB32), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1 VARIANT_IN_GENE ZBTB32 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr19",
"pos": 29661858,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.42066... | [
{
"source_db": "ClinVar",
"source_id": "ZBTB32",
"text": "GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1 VARIANT_IN_GENE ZBTB32",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1",
"gene": "ZBTB32",
"mean_phylop": -0.16,
"track": "phyloP100way"
} | 1 |
co_cons_00163 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 1p36.32-36.22(chr1:4995984-11364920)x1 (in gene ACOT7), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 1p36.32-36.22(chr1:4995984-11364920)x1 VARIANT_IN_GENE ACOT7 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 1p36.32-36.22(chr1:4995984-11364920)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 1p36.32-36.22(chr1:4995984-11364920)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 1p36.32-36.22(chr1:4995984-11364920)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 4995984,
"track": "phyloP100way",
"window": 20,
"scores": [
0.141488,
... | [
{
"source_db": "ClinVar",
"source_id": "ACOT7",
"text": "GRCh37/hg19 1p36.32-36.22(chr1:4995984-11364920)x1 VARIANT_IN_GENE ACOT7",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 1p36.32-36.22(chr1:4995984-11364920)x1",
"gene": "ACOT7",
"mean_phylop": -0.016,
"track": "phyloP100way"
} | 1 |
co_cons_00164 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399) (in gene ABHD17B), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399) VARIANT_IN_GENE ABHD17B | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 203861,
"track": "phyloP100way",
"window": 20,
"scores": [
0.643575,
... | [
{
"source_db": "ClinVar",
"source_id": "ABHD17B",
"text": "GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399) VARIANT_IN_GENE ABHD17B",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 9p24.3-q21.32(chr9:203861-84155399)",
"gene": "ABHD17B",
"mean_phylop": -0.04,
"track": "phyloP100way"
} | 1 |
co_cons_00165 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_020311.3(ACKR3):c.772G>A (p.Val258Met) (in gene ACKR3), classify the evolutionary constraint across the variant's genomic window. | NM_020311.3(ACKR3):c.772G>A (p.Val258Met) VARIANT_IN_GENE ACKR3 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_020311.3(ACKR3):c.772G>A (p.Val258Met)",
"source_node_type": "VARIANT",
"source_node_label": "NM_020311.3(ACKR3):c.772G>A (p.Val258Met)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_020311.3(ACKR3):c.772G>A (p.Val258Met)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 236581237,
"track": "phyloP100way",
"window": 20,
"scores": [
7.64583,
... | [
{
"source_db": "ClinVar",
"source_id": "ACKR3",
"text": "NM_020311.3(ACKR3):c.772G>A (p.Val258Met) VARIANT_IN_GENE ACKR3",
"confidence": 1
}
] | {
"variant": "NM_020311.3(ACKR3):c.772G>A (p.Val258Met)",
"gene": "ACKR3",
"mean_phylop": 3.93,
"track": "phyloP100way"
} | 1 |
co_cons_00166 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_022552.5(DNMT3A):c.2322+1G>A (in gene DNMT3A), classify the evolutionary constraint across the variant's genomic window. | NM_022552.5(DNMT3A):c.2322+1G>A VARIANT_IN_GENE DNMT3A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_022552.5(DNMT3A):c.2322+1G>A",
"source_node_type": "VARIANT",
"source_node_label": "NM_022552.5(DNMT3A):c.2322+1G>A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_sour... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_022552.5(DNMT3A):c.2322+1G>A",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 25240301,
"track": "phyloP100way",
"window": 20,
"scores": [
0.42837000000000003,
... | [
{
"source_db": "ClinVar",
"source_id": "DNMT3A",
"text": "NM_022552.5(DNMT3A):c.2322+1G>A VARIANT_IN_GENE DNMT3A",
"confidence": 1
}
] | {
"variant": "NM_022552.5(DNMT3A):c.2322+1G>A",
"gene": "DNMT3A",
"mean_phylop": 3.8970000000000002,
"track": "phyloP100way"
} | 1 |
co_cons_00167 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_002087.4(GRN):c.1558G>T (p.Glu520Ter) (in gene GRN), classify the evolutionary constraint across the variant's genomic window. | NM_002087.4(GRN):c.1558G>T (p.Glu520Ter) VARIANT_IN_GENE GRN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002087.4(GRN):c.1558G>T (p.Glu520Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002087.4(GRN):c.1558G>T (p.Glu520Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_002087.4(GRN):c.1558G>T (p.Glu520Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 44352485,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.735213,
... | [
{
"source_db": "ClinVar",
"source_id": "GRN",
"text": "NM_002087.4(GRN):c.1558G>T (p.Glu520Ter) VARIANT_IN_GENE GRN",
"confidence": 1
}
] | {
"variant": "NM_002087.4(GRN):c.1558G>T (p.Glu520Ter)",
"gene": "GRN",
"mean_phylop": 0.069,
"track": "phyloP100way"
} | 1 |
co_cons_00168 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001101.5(ACTB):c.586C>G (p.Arg196Gly) (in gene ACTB), classify the evolutionary constraint across the variant's genomic window. | NM_001101.5(ACTB):c.586C>G (p.Arg196Gly) VARIANT_IN_GENE ACTB | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001101.5(ACTB):c.586C>G (p.Arg196Gly)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001101.5(ACTB):c.586C>G (p.Arg196Gly)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001101.5(ACTB):c.586C>G (p.Arg196Gly)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 5528497,
"track": "phyloP100way",
"window": 20,
"scores": [
5.23775,
9.5... | [
{
"source_db": "ClinVar",
"source_id": "ACTB",
"text": "NM_001101.5(ACTB):c.586C>G (p.Arg196Gly) VARIANT_IN_GENE ACTB",
"confidence": 1
}
] | {
"variant": "NM_001101.5(ACTB):c.586C>G (p.Arg196Gly)",
"gene": "ACTB",
"mean_phylop": 6.46,
"track": "phyloP100way"
} | 1 |
co_cons_00169 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_003054.4(SLC18A2):c.835_836delAG (in gene SLC18A2), classify the evolutionary constraint across the variant's genomic window. | NM_003054.4(SLC18A2):c.835_836delAG VARIANT_IN_GENE SLC18A2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_003054.4(SLC18A2):c.835_836delAG",
"source_node_type": "VARIANT",
"source_node_label": "NM_003054.4(SLC18A2):c.835_836delAG",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"e... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_003054.4(SLC18A2):c.835_836delAG",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 117255595,
"track": "phyloP100way",
"window": 20,
"scores": [
7.71109,
-4.10... | [
{
"source_db": "ClinVar",
"source_id": "SLC18A2",
"text": "NM_003054.4(SLC18A2):c.835_836delAG VARIANT_IN_GENE SLC18A2",
"confidence": 1
}
] | {
"variant": "NM_003054.4(SLC18A2):c.835_836delAG",
"gene": "SLC18A2",
"mean_phylop": 2.583,
"track": "phyloP100way"
} | 1 |
co_cons_00170 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 18q21.32-23(chr18:58525322-78005236)x3 (in gene ADNP2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 18q21.32-23(chr18:58525322-78005236)x3 VARIANT_IN_GENE ADNP2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 18q21.32-23(chr18:58525322-78005236)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 18q21.32-23(chr18:58525322-78005236)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 18q21.32-23(chr18:58525322-78005236)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr18",
"pos": 58525322,
"track": "phyloP100way",
"window": 20,
"scores": [
0.144583... | [
{
"source_db": "ClinVar",
"source_id": "ADNP2",
"text": "GRCh37/hg19 18q21.32-23(chr18:58525322-78005236)x3 VARIANT_IN_GENE ADNP2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 18q21.32-23(chr18:58525322-78005236)x3",
"gene": "ADNP2",
"mean_phylop": -0.171,
"track": "phyloP100way"
} | 1 |
co_cons_00171 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 7q36.1-36.3(chr7:150802801-159335866)x1 (in gene ABCB8), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 7q36.1-36.3(chr7:150802801-159335866)x1 VARIANT_IN_GENE ABCB8 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 7q36.1-36.3(chr7:150802801-159335866)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 7q36.1-36.3(chr7:150802801-159335866)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 7q36.1-36.3(chr7:150802801-159335866)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 150802801,
"track": "phyloP100way",
"window": 20,
"scores": [
0.35770... | [
{
"source_db": "ClinVar",
"source_id": "ABCB8",
"text": "GRCh38/hg38 7q36.1-36.3(chr7:150802801-159335866)x1 VARIANT_IN_GENE ABCB8",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 7q36.1-36.3(chr7:150802801-159335866)x1",
"gene": "ABCB8",
"mean_phylop": -0.111,
"track": "phyloP100way"
} | 1 |
co_cons_00172 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 2q22.3-24.1(chr2:143900149-158321624)x3 (in gene CYTIP), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 2q22.3-24.1(chr2:143900149-158321624)x3 VARIANT_IN_GENE CYTIP | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 2q22.3-24.1(chr2:143900149-158321624)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 2q22.3-24.1(chr2:143900149-158321624)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 2q22.3-24.1(chr2:143900149-158321624)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 143900149,
"track": "phyloP100way",
"window": 20,
"scores": [
0.57108... | [
{
"source_db": "ClinVar",
"source_id": "CYTIP",
"text": "GRCh38/hg38 2q22.3-24.1(chr2:143900149-158321624)x3 VARIANT_IN_GENE CYTIP",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 2q22.3-24.1(chr2:143900149-158321624)x3",
"gene": "CYTIP",
"mean_phylop": 0.528,
"track": "phyloP100way"
} | 1 |
co_cons_00173 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000249.4(MLH1):c.1410-2A>G (in gene MLH1), classify the evolutionary constraint across the variant's genomic window. | NM_000249.4(MLH1):c.1410-2A>G VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.1410-2A>G",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.1410-2A>G",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_d... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000249.4(MLH1):c.1410-2A>G",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 37028782,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.517559,
-0.807591,
... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.1410-2A>G VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.1410-2A>G",
"gene": "MLH1",
"mean_phylop": 1.609,
"track": "phyloP100way"
} | 1 |
co_cons_00174 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000021.4(PSEN1):c.263C>G (p.Pro88Arg) (in gene PSEN1), classify the evolutionary constraint across the variant's genomic window. | NM_000021.4(PSEN1):c.263C>G (p.Pro88Arg) VARIANT_IN_GENE PSEN1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000021.4(PSEN1):c.263C>G (p.Pro88Arg)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000021.4(PSEN1):c.263C>G (p.Pro88Arg)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000021.4(PSEN1):c.263C>G (p.Pro88Arg)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 73170972,
"track": "phyloP100way",
"window": 20,
"scores": [
0.885717,
... | [
{
"source_db": "ClinVar",
"source_id": "PSEN1",
"text": "NM_000021.4(PSEN1):c.263C>G (p.Pro88Arg) VARIANT_IN_GENE PSEN1",
"confidence": 1
}
] | {
"variant": "NM_000021.4(PSEN1):c.263C>G (p.Pro88Arg)",
"gene": "PSEN1",
"mean_phylop": 6.08,
"track": "phyloP100way"
} | 1 |
co_cons_00175 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1 (in gene ADIRF), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1 VARIANT_IN_GENE ADIRF | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 79898516,
"track": "phyloP100way",
"window": 20,
"scores": [
1.13222... | [
{
"source_db": "ClinVar",
"source_id": "ADIRF",
"text": "GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1 VARIANT_IN_GENE ADIRF",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 10q22.3-23.2(chr10:79898516-87109827)x1",
"gene": "ADIRF",
"mean_phylop": 0.34500000000000003,
"track": "phyloP100way"
} | 1 |
co_cons_00176 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 16q12.2-22.2(chr16:54416050-72453266)x3 (in gene ARL2BP), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 16q12.2-22.2(chr16:54416050-72453266)x3 VARIANT_IN_GENE ARL2BP | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 16q12.2-22.2(chr16:54416050-72453266)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 16q12.2-22.2(chr16:54416050-72453266)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 16q12.2-22.2(chr16:54416050-72453266)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 54416050,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.1267... | [
{
"source_db": "ClinVar",
"source_id": "ARL2BP",
"text": "GRCh37/hg19 16q12.2-22.2(chr16:54416050-72453266)x3 VARIANT_IN_GENE ARL2BP",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 16q12.2-22.2(chr16:54416050-72453266)x3",
"gene": "ARL2BP",
"mean_phylop": -0.147,
"track": "phyloP100way"
} | 1 |
co_cons_00177 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 7p14.2-13(chr7:36499426-43428961)x1 (in gene AMPH), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 7p14.2-13(chr7:36499426-43428961)x1 VARIANT_IN_GENE AMPH | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 7p14.2-13(chr7:36499426-43428961)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 7p14.2-13(chr7:36499426-43428961)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 7p14.2-13(chr7:36499426-43428961)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 36499426,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.962558999... | [
{
"source_db": "ClinVar",
"source_id": "AMPH",
"text": "GRCh37/hg19 7p14.2-13(chr7:36499426-43428961)x1 VARIANT_IN_GENE AMPH",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 7p14.2-13(chr7:36499426-43428961)x1",
"gene": "AMPH",
"mean_phylop": -0.404,
"track": "phyloP100way"
} | 1 |
co_cons_00178 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_014043.4(CHMP2B):c.618A>T (p.Gln206His) (in gene CHMP2B), classify the evolutionary constraint across the variant's genomic window. | NM_014043.4(CHMP2B):c.618A>T (p.Gln206His) VARIANT_IN_GENE CHMP2B | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_014043.4(CHMP2B):c.618A>T (p.Gln206His)",
"source_node_type": "VARIANT",
"source_node_label": "NM_014043.4(CHMP2B):c.618A>T (p.Gln206His)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_014043.4(CHMP2B):c.618A>T (p.Gln206His)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 87253798,
"track": "phyloP100way",
"window": 20,
"scores": [
9.121,
8.... | [
{
"source_db": "ClinVar",
"source_id": "CHMP2B",
"text": "NM_014043.4(CHMP2B):c.618A>T (p.Gln206His) VARIANT_IN_GENE CHMP2B",
"confidence": 1
}
] | {
"variant": "NM_014043.4(CHMP2B):c.618A>T (p.Gln206His)",
"gene": "CHMP2B",
"mean_phylop": 5.449,
"track": "phyloP100way"
} | 1 |
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