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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
no_tiss_00225 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is FLT3 most highly expressed? | FLT3 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere | {
"steps": [
{
"hop": 1,
"source_node_id": "FLT3",
"source_node_type": "GENE",
"source_node_label": "FLT3",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4572315624,
"edge_source_db": "GTEx",
"target_node... | B | [
"A. Kidney_Medulla",
"B. Brain_Cerebellar_Hemisphere",
"C. Cells_Cultured_fibroblasts",
"D. Muscle_Skeletal"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FLT3",
"source_db": "UniProt",
"payload": {
"accession": "P36888",
"sequence": "MPALARDGGQLPLLVVFSAMIFGTITNQDLPVIKCVLINHKNNDSSVGKSSSYPMVSESPEDLGCALRPQSSGTVYEAAAVEVDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMT... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellar_Hemisphere",
"text": "FLT3 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere",
"confidence": 0.4572315624
}
] | {
"gene": "FLT3",
"top_tissue": "Brain_Cerebellar_Hemisphere",
"top_tpm": 22.5447
} | 0.457232 |
no_tiss_00226 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ETV1 most highly expressed? | ETV1 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere | {
"steps": [
{
"hop": 1,
"source_node_id": "ETV1",
"source_node_type": "GENE",
"source_node_label": "ETV1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.7480657733,
"edge_source_db": "GTEx",
"target_node... | A | [
"A. Brain_Cerebellar_Hemisphere",
"B. Cells_EBV-transformed_lymphocytes",
"C. Muscle_Skeletal",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ETV1",
"source_db": "UniProt",
"payload": {
"accession": "P50549",
"sequence": "MDGFYDQQVPYMVTNSQRGRNCNEKPTNVRKRKFINRDLAHDSEELFQDLSQLQETWLAEAQVPDNDEQFVPDYQAESLAFHGLPLKIKKEPHSPCSEISSACSQEQPFKFSYGEKCLYNVSAYDQKPQVGMRP... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellar_Hemisphere",
"text": "ETV1 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere",
"confidence": 0.7480657733
}
] | {
"gene": "ETV1",
"top_tissue": "Brain_Cerebellar_Hemisphere",
"top_tpm": 174.599
} | 0.748066 |
no_tiss_00227 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is PSEN2 most highly expressed? | PSEN2 GENE_EXPRESSED_IN_TISSUE Uterus | {
"steps": [
{
"hop": 1,
"source_node_id": "PSEN2",
"source_node_type": "GENE",
"source_node_label": "PSEN2",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4670090578,
"edge_source_db": "GTEx",
"target_no... | C | [
"A. Liver",
"B. Brain_Hippocampus",
"C. Uterus",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PSEN2",
"source_db": "UniProt",
"payload": {
"accession": "P49810",
"sequence": "MLTFMASDSEEEVCDERTSLMSAESPTPRSCQEGRQGPEDGENTAQWRSQENEEDGEEDPDRYVCSGVPGRPPGLEEELTLKYGAKHVIMLFVPVTLCMIVVVATIKSVRFYTEKNGQLIYTPFTEDTPSVGQ... | [
{
"source_db": "GTEx",
"source_id": "Uterus",
"text": "PSEN2 GENE_EXPRESSED_IN_TISSUE Uterus",
"confidence": 0.4670090578
}
] | {
"gene": "PSEN2",
"top_tissue": "Uterus",
"top_tpm": 24.1901
} | 0.467009 |
no_tiss_00228 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ETV1 most highly expressed? | ETV1 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere | {
"steps": [
{
"hop": 1,
"source_node_id": "ETV1",
"source_node_type": "GENE",
"source_node_label": "ETV1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.7480657733,
"edge_source_db": "GTEx",
"target_node... | A | [
"A. Brain_Cerebellar_Hemisphere",
"B. Muscle_Skeletal",
"C. Cells_EBV-transformed_lymphocytes",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ETV1",
"source_db": "UniProt",
"payload": {
"accession": "P50549",
"sequence": "MDGFYDQQVPYMVTNSQRGRNCNEKPTNVRKRKFINRDLAHDSEELFQDLSQLQETWLAEAQVPDNDEQFVPDYQAESLAFHGLPLKIKKEPHSPCSEISSACSQEQPFKFSYGEKCLYNVSAYDQKPQVGMRP... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellar_Hemisphere",
"text": "ETV1 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere",
"confidence": 0.7480657733
}
] | {
"gene": "ETV1",
"top_tissue": "Brain_Cerebellar_Hemisphere",
"top_tpm": 174.599
} | 0.748066 |
no_tiss_00229 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is CDC25B most highly expressed? | CDC25B GENE_EXPRESSED_IN_TISSUE Brain_Cerebellum | {
"steps": [
{
"hop": 1,
"source_node_id": "CDC25B",
"source_node_type": "GENE",
"source_node_label": "CDC25B",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.7199849551,
"edge_source_db": "GTEx",
"target_... | D | [
"A. Heart_Left_Ventricle",
"B. Pancreas",
"C. Muscle_Skeletal",
"D. Brain_Cerebellum"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDC25B",
"source_db": "UniProt",
"payload": {
"accession": "P30305",
"sequence": "MEVPQPEPAPGSALSPAGVCGGAQRPGHLPGLLLGSHGLLGSPVRAAASSPVTTLTQTMHDLAGLGSETPKSQVGTLLFRSRSRLTHLSLSRRASESSLSSESSESSDAGLCMDSPSPMDPHMAEQTFEQAI... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellum",
"text": "CDC25B GENE_EXPRESSED_IN_TISSUE Brain_Cerebellum",
"confidence": 0.7199849551
}
] | {
"gene": "CDC25B",
"top_tissue": "Brain_Cerebellum",
"top_tpm": 143.633
} | 0.719985 |
no_tiss_00230 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is KRAS most highly expressed? | KRAS GENE_EXPRESSED_IN_TISSUE Nerve_Tibial | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5004468095,
"edge_source_db": "GTEx",
"target_node... | D | [
"A. Heart_Left_Ventricle",
"B. Pancreas",
"C. Muscle_Skeletal",
"D. Nerve_Tibial"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "GTEx",
"source_id": "Nerve_Tibial",
"text": "KRAS GENE_EXPRESSED_IN_TISSUE Nerve_Tibial",
"confidence": 0.5004468095
}
] | {
"gene": "KRAS",
"top_tissue": "Nerve_Tibial",
"top_tpm": 30.7364
} | 0.500447 |
no_tiss_00231 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is DNAJC6 most highly expressed? | DNAJC6 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere | {
"steps": [
{
"hop": 1,
"source_node_id": "DNAJC6",
"source_node_type": "GENE",
"source_node_label": "DNAJC6",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.6360673154,
"edge_source_db": "GTEx",
"target_... | A | [
"A. Brain_Cerebellar_Hemisphere",
"B. Liver",
"C. Muscle_Skeletal",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "DNAJC6",
"source_db": "UniProt",
"payload": {
"accession": "O75061",
"sequence": "MKDSENKGASSPDMEPSYGGGLFDMVKGGAGRLFSNLKDNLKDTLKDTSSRVIQSVTSYTKGDLDFTYVTSRIIVMSFPLDNVDIGFRNQVDDIRSFLDSRHLDHYTVYNLSPKSYRTAKFHSRVSECSWPI... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellar_Hemisphere",
"text": "DNAJC6 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere",
"confidence": 0.6360673154
}
] | {
"gene": "DNAJC6",
"top_tissue": "Brain_Cerebellar_Hemisphere",
"top_tpm": 79.9987
} | 0.636067 |
no_tiss_00232 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ABL1 most highly expressed? | ABL1 GENE_EXPRESSED_IN_TISSUE Colon_Sigmoid | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.7408710894,
"edge_source_db": "GTEx",
"target_node... | C | [
"A. Whole_Blood",
"B. Liver",
"C. Colon_Sigmoid",
"D. Pancreas"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "GTEx",
"source_id": "Colon_Sigmoid",
"text": "ABL1 GENE_EXPRESSED_IN_TISSUE Colon_Sigmoid",
"confidence": 0.7408710894
}
] | {
"gene": "ABL1",
"top_tissue": "Colon_Sigmoid",
"top_tpm": 166.084
} | 0.740871 |
no_tiss_00233 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is POLD1 most highly expressed? | POLD1 GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes | {
"steps": [
{
"hop": 1,
"source_node_id": "POLD1",
"source_node_type": "GENE",
"source_node_label": "POLD1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5929527908,
"edge_source_db": "GTEx",
"target_no... | A | [
"A. Cells_EBV-transformed_lymphocytes",
"B. Brain_Anterior_cingulate_cortex_BA24",
"C. Brain_Hippocampus",
"D. Brain_Amygdala"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "POLD1",
"source_db": "UniProt",
"payload": {
"accession": "P28340",
"sequence": "MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQSVLEGVADGQVPPSAIDPRWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRGSVPVLRAFGVTDE... | [
{
"source_db": "GTEx",
"source_id": "Cells_EBV-transformed_lymphocytes",
"text": "POLD1 GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes",
"confidence": 0.5929527908
}
] | {
"gene": "POLD1",
"top_tissue": "Cells_EBV-transformed_lymphocytes",
"top_tpm": 59.1334
} | 0.592953 |
no_tiss_00234 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is NLRP3 most highly expressed? | NLRP3 GENE_EXPRESSED_IN_TISSUE Whole_Blood | {
"steps": [
{
"hop": 1,
"source_node_id": "NLRP3",
"source_node_type": "GENE",
"source_node_label": "NLRP3",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4618579192,
"edge_source_db": "GTEx",
"target_no... | D | [
"A. Cells_EBV-transformed_lymphocytes",
"B. Cells_Cultured_fibroblasts",
"C. Pancreas",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NLRP3",
"source_db": "UniProt",
"payload": {
"accession": "Q96P20",
"sequence": "MKMASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPKWGSDNARVSNPTVICQEDSIEEEWMGLLEYLSRISICKMK... | [
{
"source_db": "GTEx",
"source_id": "Whole_Blood",
"text": "NLRP3 GENE_EXPRESSED_IN_TISSUE Whole_Blood",
"confidence": 0.4618579192
}
] | {
"gene": "NLRP3",
"top_tissue": "Whole_Blood",
"top_tpm": 23.3094
} | 0.461858 |
no_tiss_00235 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ASXL1 most highly expressed? | ASXL1 GENE_EXPRESSED_IN_TISSUE Nerve_Tibial | {
"steps": [
{
"hop": 1,
"source_node_id": "ASXL1",
"source_node_type": "GENE",
"source_node_label": "ASXL1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.6013536924,
"edge_source_db": "GTEx",
"target_no... | C | [
"A. Brain_Substantia_nigra",
"B. Brain_Putamen_basal_ganglia",
"C. Nerve_Tibial",
"D. Brain_Amygdala"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASXL1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IXJ9",
"sequence": "MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGTSPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGEEPEDTADVESCGSNEASTVSGENDVSLDETSSN... | [
{
"source_db": "GTEx",
"source_id": "Nerve_Tibial",
"text": "ASXL1 GENE_EXPRESSED_IN_TISSUE Nerve_Tibial",
"confidence": 0.6013536924
}
] | {
"gene": "ASXL1",
"top_tissue": "Nerve_Tibial",
"top_tpm": 62.7268
} | 0.601354 |
no_tiss_00236 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is C9orf72 most highly expressed? | C9orf72 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere | {
"steps": [
{
"hop": 1,
"source_node_id": "C9orf72",
"source_node_type": "GENE",
"source_node_label": "C9orf72",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5667436612,
"edge_source_db": "GTEx",
"targe... | A | [
"A. Brain_Cerebellar_Hemisphere",
"B. Heart_Left_Ventricle",
"C. Liver",
"D. Kidney_Cortex"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "C9orf72",
"source_db": "UniProt",
"payload": {
"accession": "Q96LT7",
"sequence": "MSTLCPPPSPAVAKTEIALSGKSPLLAATFAYWDNILGPRVRHIWAPKTEQVLLSDGEITFLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGNWNGDRSTYGLSIILPQTELSFYLPLHRVC... | [
{
"source_db": "GTEx",
"source_id": "Brain_Cerebellar_Hemisphere",
"text": "C9orf72 GENE_EXPRESSED_IN_TISSUE Brain_Cerebellar_Hemisphere",
"confidence": 0.5667436612
}
] | {
"gene": "C9orf72",
"top_tissue": "Brain_Cerebellar_Hemisphere",
"top_tpm": 49.1738
} | 0.566744 |
no_tiss_00237 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is LRRK2 most highly expressed? | LRRK2 GENE_EXPRESSED_IN_TISSUE Lung | {
"steps": [
{
"hop": 1,
"source_node_id": "LRRK2",
"source_node_type": "GENE",
"source_node_label": "LRRK2",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4955052268,
"edge_source_db": "GTEx",
"target_no... | C | [
"A. Liver",
"B. Testis",
"C. Lung",
"D. Heart_Left_Ventricle"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LRRK2",
"source_db": "UniProt",
"payload": {
"accession": "Q5S007",
"sequence": "MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSV... | [
{
"source_db": "GTEx",
"source_id": "Lung",
"text": "LRRK2 GENE_EXPRESSED_IN_TISSUE Lung",
"confidence": 0.4955052268
}
] | {
"gene": "LRRK2",
"top_tissue": "Lung",
"top_tpm": 29.6712
} | 0.495505 |
no_tiss_00238 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ATM most highly expressed? | ATM GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4475955638,
"edge_source_db": "GTEx",
"target_node_i... | D | [
"A. Brain_Anterior_cingulate_cortex_BA24",
"B. Muscle_Skeletal",
"C. Heart_Left_Ventricle",
"D. Cells_EBV-transformed_lymphocytes"
] | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "GTEx",
"source_id": "Cells_EBV-transformed_lymphocytes",
"text": "ATM GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes",
"confidence": 0.4475955638
}
] | {
"gene": "ATM",
"top_tissue": "Cells_EBV-transformed_lymphocytes",
"top_tpm": 21.0283
} | 0.447596 |
no_tiss_00239 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ADRA2B most highly expressed? | ADRA2B GENE_EXPRESSED_IN_TISSUE Spleen | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2B",
"source_node_type": "GENE",
"source_node_label": "ADRA2B",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.3832217577,
"edge_source_db": "GTEx",
"target_... | D | [
"A. Cells_EBV-transformed_lymphocytes",
"B. Whole_Blood",
"C. Cells_Cultured_fibroblasts",
"D. Spleen"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2B",
"source_db": "UniProt",
"payload": {
"accession": "P18089",
"sequence": "MDHQDPYSVQATAAIAAAITFLILFTIFGNALVILAVLTSRSLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIVHLCAISLDRYWAVSRALEYNSKRTPRRIKCI... | [
{
"source_db": "GTEx",
"source_id": "Spleen",
"text": "ADRA2B GENE_EXPRESSED_IN_TISSUE Spleen",
"confidence": 0.3832217577
}
] | {
"gene": "ADRA2B",
"top_tissue": "Spleen",
"top_tpm": 13.1199
} | 0.383222 |
no_tiss_00240 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ACO2 most highly expressed? | ACO2 GENE_EXPRESSED_IN_TISSUE Muscle_Skeletal | {
"steps": [
{
"hop": 1,
"source_node_id": "ACO2",
"source_node_type": "GENE",
"source_node_label": "ACO2",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.8121290683,
"edge_source_db": "GTEx",
"target_node... | B | [
"A. Liver",
"B. Muscle_Skeletal",
"C. Pancreas",
"D. Whole_Blood"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACO2",
"source_db": "UniProt",
"payload": {
"accession": "Q99798",
"sequence": "MAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPNEYIHYDLLEKNINIVRKRLNRPLTLSEKIVYGHLDDPASQEIERGKSYLRLRPDRVAMQDATAQMAMLQFISSGLSKVAVPSTIHCDHLIEAQV... | [
{
"source_db": "GTEx",
"source_id": "Muscle_Skeletal",
"text": "ACO2 GENE_EXPRESSED_IN_TISSUE Muscle_Skeletal",
"confidence": 0.8121290683
}
] | {
"gene": "ACO2",
"top_tissue": "Muscle_Skeletal",
"top_tpm": 272.363
} | 0.812129 |
no_tiss_00241 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is PIK3CA most highly expressed? | PIK3CA GENE_EXPRESSED_IN_TISSUE Artery_Tibial | {
"steps": [
{
"hop": 1,
"source_node_id": "PIK3CA",
"source_node_type": "GENE",
"source_node_label": "PIK3CA",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4611308705,
"edge_source_db": "GTEx",
"target_... | D | [
"A. Pancreas",
"B. Brain_Hippocampus",
"C. Brain_Putamen_basal_ganglia",
"D. Artery_Tibial"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PIK3CA",
"source_db": "UniProt",
"payload": {
"accession": "P42336",
"sequence": "MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVK... | [
{
"source_db": "GTEx",
"source_id": "Artery_Tibial",
"text": "PIK3CA GENE_EXPRESSED_IN_TISSUE Artery_Tibial",
"confidence": 0.4611308705
}
] | {
"gene": "PIK3CA",
"top_tissue": "Artery_Tibial",
"top_tpm": 23.1876
} | 0.461131 |
no_tiss_00242 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is RAD51C most highly expressed? | RAD51C GENE_EXPRESSED_IN_TISSUE Testis | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51C",
"source_node_type": "GENE",
"source_node_label": "RAD51C",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.3900992477,
"edge_source_db": "GTEx",
"target_... | A | [
"A. Testis",
"B. Pancreas",
"C. Whole_Blood",
"D. Liver"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51C",
"source_db": "UniProt",
"payload": {
"accession": "O43502",
"sequence": "MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKT... | [
{
"source_db": "GTEx",
"source_id": "Testis",
"text": "RAD51C GENE_EXPRESSED_IN_TISSUE Testis",
"confidence": 0.3900992477
}
] | {
"gene": "RAD51C",
"top_tissue": "Testis",
"top_tpm": 13.807
} | 0.390099 |
no_tiss_00243 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is ABL1 most highly expressed? | ABL1 GENE_EXPRESSED_IN_TISSUE Colon_Sigmoid | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.7408710894,
"edge_source_db": "GTEx",
"target_node... | B | [
"A. Liver",
"B. Colon_Sigmoid",
"C. Whole_Blood",
"D. Pancreas"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "GTEx",
"source_id": "Colon_Sigmoid",
"text": "ABL1 GENE_EXPRESSED_IN_TISSUE Colon_Sigmoid",
"confidence": 0.7408710894
}
] | {
"gene": "ABL1",
"top_tissue": "Colon_Sigmoid",
"top_tpm": 166.084
} | 0.740871 |
no_tiss_00244 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is NOTCH1 most highly expressed? | NOTCH1 GENE_EXPRESSED_IN_TISSUE Lung | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.5618645496,
"edge_source_db": "GTEx",
"target_... | D | [
"A. Muscle_Skeletal",
"B. Brain_Cerebellar_Hemisphere",
"C. Adrenal_Gland",
"D. Lung"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "GTEx",
"source_id": "Lung",
"text": "NOTCH1 GENE_EXPRESSED_IN_TISSUE Lung",
"confidence": 0.5618645496
}
] | {
"gene": "NOTCH1",
"top_tissue": "Lung",
"top_tpm": 47.5107
} | 0.561865 |
no_tiss_00245 | tissue_specific | noncoding_regulatory | easy | 1 | According to GTEx v8, in which tissue is PMS2 most highly expressed? | PMS2 GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "GENE_EXPRESSED_IN_TISSUE",
"edge_evidence_type": "expression",
"edge_confidence": 0.4560042266,
"edge_source_db": "GTEx",
"target_node... | D | [
"A. Whole_Blood",
"B. Pancreas",
"C. Heart_Left_Ventricle",
"D. Cells_EBV-transformed_lymphocytes"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "GTEx",
"source_id": "Cells_EBV-transformed_lymphocytes",
"text": "PMS2 GENE_EXPRESSED_IN_TISSUE Cells_EBV-transformed_lymphocytes",
"confidence": 0.4560042266
}
] | {
"gene": "PMS2",
"top_tissue": "Cells_EBV-transformed_lymphocytes",
"top_tpm": 22.3459
} | 0.456004 |
co_cons_00000 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 3q26.31-29(chr3:171558472-197871052)x3 (in gene ABCC5), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 3q26.31-29(chr3:171558472-197871052)x3 VARIANT_IN_GENE ABCC5 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 3q26.31-29(chr3:171558472-197871052)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 3q26.31-29(chr3:171558472-197871052)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | 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": "GRCh37/hg19 3q26.31-29(chr3:171558472-197871052)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 171549421,
"track": "phyloP100way",
"window": 20,
"scores": [
0.164834... | [
{
"source_db": "ClinVar",
"source_id": "ABCC5",
"text": "GRCh37/hg19 3q26.31-29(chr3:171558472-197871052)x3 VARIANT_IN_GENE ABCC5",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 3q26.31-29(chr3:171558472-197871052)x3",
"gene": "ABCC5",
"mean_phylop": 0.224,
"track": "phyloP100way"
} | 1 |
co_cons_00001 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000157.4(GBA1):c.1343A>T (p.Asp448Val) (in gene LOC106627981), classify the evolutionary constraint across the variant's genomic window. | NM_000157.4(GBA1):c.1343A>T (p.Asp448Val) VARIANT_IN_GENE LOC106627981 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000157.4(GBA1):c.1343A>T (p.Asp448Val)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000157.4(GBA1):c.1343A>T (p.Asp448Val)",
"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.1343A>T (p.Asp448Val)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 155235726,
"track": "phyloP100way",
"window": 20,
"scores": [
1.89641,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC106627981",
"text": "NM_000157.4(GBA1):c.1343A>T (p.Asp448Val) VARIANT_IN_GENE LOC106627981",
"confidence": 1
}
] | {
"variant": "NM_000157.4(GBA1):c.1343A>T (p.Asp448Val)",
"gene": "LOC106627981",
"mean_phylop": 3.7279999999999998,
"track": "phyloP100way"
} | 1 |
co_cons_00002 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001904.4(CTNNB1):c.942del (p.Ile315fs) (in gene CTNNB1), classify the evolutionary constraint across the variant's genomic window. | NM_001904.4(CTNNB1):c.942del (p.Ile315fs) VARIANT_IN_GENE CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001904.4(CTNNB1):c.942del (p.Ile315fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001904.4(CTNNB1):c.942del (p.Ile315fs)",
"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_001904.4(CTNNB1):c.942del (p.Ile315fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 41227213,
"track": "phyloP100way",
"window": 20,
"scores": [
0.167205,
... | [
{
"source_db": "ClinVar",
"source_id": "CTNNB1",
"text": "NM_001904.4(CTNNB1):c.942del (p.Ile315fs) VARIANT_IN_GENE CTNNB1",
"confidence": 1
}
] | {
"variant": "NM_001904.4(CTNNB1):c.942del (p.Ile315fs)",
"gene": "CTNNB1",
"mean_phylop": 4.276,
"track": "phyloP100way"
} | 1 |
co_cons_00003 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000044.6(AR):c.2491C>T (p.Leu831Phe) (in gene AR), classify the evolutionary constraint across the variant's genomic window. | NM_000044.6(AR):c.2491C>T (p.Leu831Phe) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.2491C>T (p.Leu831Phe)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.2491C>T (p.Leu831Phe)",
"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_000044.6(AR):c.2491C>T (p.Leu831Phe)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 67722868,
"track": "phyloP100way",
"window": 20,
"scores": [
4.98443,
1.4... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.2491C>T (p.Leu831Phe) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.2491C>T (p.Leu831Phe)",
"gene": "AR",
"mean_phylop": 4.943,
"track": "phyloP100way"
} | 1 |
co_cons_00004 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000004.12:g.169508332del (in gene NEK1), classify the evolutionary constraint across the variant's genomic window. | NC_000004.12:g.169508332del VARIANT_IN_GENE NEK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000004.12:g.169508332del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000004.12:g.169508332del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": ... | 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": "NC_000004.12:g.169508332del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 169508331,
"track": "phyloP100way",
"window": 20,
"scores": [
0.323575,
2.37539,
... | [
{
"source_db": "ClinVar",
"source_id": "NEK1",
"text": "NC_000004.12:g.169508332del VARIANT_IN_GENE NEK1",
"confidence": 1
}
] | {
"variant": "NC_000004.12:g.169508332del",
"gene": "NEK1",
"mean_phylop": 2.238,
"track": "phyloP100way"
} | 1 |
co_cons_00005 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)x1 (in gene BAZ1A), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)x1 VARIANT_IN_GENE BAZ1A | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)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": "GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 33880412,
"track": "phyloP100way",
"window": 20,
"scores": [
0.16181... | [
{
"source_db": "ClinVar",
"source_id": "BAZ1A",
"text": "GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)x1 VARIANT_IN_GENE BAZ1A",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 14q13.1-21.1(chr14:33880412-42359485)x1",
"gene": "BAZ1A",
"mean_phylop": 0.068,
"track": "phyloP100way"
} | 1 |
co_cons_00006 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_177924.5(ASAH1):c.952C>T (p.Gln318Ter) (in gene ASAH1), classify the evolutionary constraint across the variant's genomic window. | NM_177924.5(ASAH1):c.952C>T (p.Gln318Ter) VARIANT_IN_GENE ASAH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_177924.5(ASAH1):c.952C>T (p.Gln318Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_177924.5(ASAH1):c.952C>T (p.Gln318Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | 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_177924.5(ASAH1):c.952C>T (p.Gln318Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 18059430,
"track": "phyloP100way",
"window": 20,
"scores": [
7.20966,
7... | [
{
"source_db": "ClinVar",
"source_id": "ASAH1",
"text": "NM_177924.5(ASAH1):c.952C>T (p.Gln318Ter) VARIANT_IN_GENE ASAH1",
"confidence": 1
}
] | {
"variant": "NM_177924.5(ASAH1):c.952C>T (p.Gln318Ter)",
"gene": "ASAH1",
"mean_phylop": 4.26,
"track": "phyloP100way"
} | 1 |
co_cons_00007 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 (in gene LOC132090669), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 VARIANT_IN_GENE LOC132090669 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)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 1q23.3-25.2(chr1:164922655-180061589)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 164922655,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0390... | [
{
"source_db": "ClinVar",
"source_id": "LOC132090669",
"text": "GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 VARIANT_IN_GENE LOC132090669",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3",
"gene": "LOC132090669",
"mean_phylop": 0.224,
"track": "phyloP100way"
} | 1 |
co_cons_00008 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3 (in gene ACTA2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3 VARIANT_IN_GENE ACTA2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3",
"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 10q21.3-23.32(chr10:69040366-93194993)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 69040366,
"track": "phyloP100way",
"window": 20,
"scores": [
0.2900... | [
{
"source_db": "ClinVar",
"source_id": "ACTA2",
"text": "GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3 VARIANT_IN_GENE ACTA2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 10q21.3-23.32(chr10:69040366-93194993)x3",
"gene": "ACTA2",
"mean_phylop": -0.027,
"track": "phyloP100way"
} | 1 |
co_cons_00009 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 Xp11.3-11.23(chrX:44182604-47607117)x1 (in gene ARAF), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 Xp11.3-11.23(chrX:44182604-47607117)x1 VARIANT_IN_GENE ARAF | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 Xp11.3-11.23(chrX:44182604-47607117)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 Xp11.3-11.23(chrX:44182604-47607117)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": "GRCh37/hg19 Xp11.3-11.23(chrX:44182604-47607117)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 44182604,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.13427,... | [
{
"source_db": "ClinVar",
"source_id": "ARAF",
"text": "GRCh37/hg19 Xp11.3-11.23(chrX:44182604-47607117)x1 VARIANT_IN_GENE ARAF",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 Xp11.3-11.23(chrX:44182604-47607117)x1",
"gene": "ARAF",
"mean_phylop": 0.28,
"track": "phyloP100way"
} | 1 |
co_cons_00010 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_006231.4(POLE):c.3632_3795+72del (in gene POLE), classify the evolutionary constraint across the variant's genomic window. | NM_006231.4(POLE):c.3632_3795+72del VARIANT_IN_GENE POLE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006231.4(POLE):c.3632_3795+72del",
"source_node_type": "VARIANT",
"source_node_label": "NM_006231.4(POLE):c.3632_3795+72del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"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",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_006231.4(POLE):c.3632_3795+72del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 132649605,
"track": "phyloP100way",
"window": 20,
"scores": [
-3.09113,
-0.4... | [
{
"source_db": "ClinVar",
"source_id": "POLE",
"text": "NM_006231.4(POLE):c.3632_3795+72del VARIANT_IN_GENE POLE",
"confidence": 1
}
] | {
"variant": "NM_006231.4(POLE):c.3632_3795+72del",
"gene": "POLE",
"mean_phylop": -0.47100000000000003,
"track": "phyloP100way"
} | 1 |
co_cons_00011 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_005612.5(REST):c.851_866del (p.Phe284fs) (in gene REST), classify the evolutionary constraint across the variant's genomic window. | NM_005612.5(REST):c.851_866del (p.Phe284fs) VARIANT_IN_GENE REST | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_005612.5(REST):c.851_866del (p.Phe284fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_005612.5(REST):c.851_866del (p.Phe284fs)",
"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_005612.5(REST):c.851_866del (p.Phe284fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 56911489,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.522079,
... | [
{
"source_db": "ClinVar",
"source_id": "REST",
"text": "NM_005612.5(REST):c.851_866del (p.Phe284fs) VARIANT_IN_GENE REST",
"confidence": 1
}
] | {
"variant": "NM_005612.5(REST):c.851_866del (p.Phe284fs)",
"gene": "REST",
"mean_phylop": 5.001,
"track": "phyloP100way"
} | 1 |
co_cons_00012 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_024675.4(PALB2):c.224_228del (p.Lys75fs) (in gene PALB2), classify the evolutionary constraint across the variant's genomic window. | NM_024675.4(PALB2):c.224_228del (p.Lys75fs) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.224_228del (p.Lys75fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.224_228del (p.Lys75fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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_024675.4(PALB2):c.224_228del (p.Lys75fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 23636318,
"track": "phyloP100way",
"window": 20,
"scores": [
1.8229700000000... | [
{
"source_db": "ClinVar",
"source_id": "PALB2",
"text": "NM_024675.4(PALB2):c.224_228del (p.Lys75fs) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.224_228del (p.Lys75fs)",
"gene": "PALB2",
"mean_phylop": 0.668,
"track": "phyloP100way"
} | 1 |
co_cons_00013 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 7q36.2-36.3(chr7:152860576-159325876)x1 (in gene BLACE), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 7q36.2-36.3(chr7:152860576-159325876)x1 VARIANT_IN_GENE BLACE | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 7q36.2-36.3(chr7:152860576-159325876)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 7q36.2-36.3(chr7:152860576-159325876)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": "GRCh38/hg38 7q36.2-36.3(chr7:152860576-159325876)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 152860576,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.118,... | [
{
"source_db": "ClinVar",
"source_id": "BLACE",
"text": "GRCh38/hg38 7q36.2-36.3(chr7:152860576-159325876)x1 VARIANT_IN_GENE BLACE",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 7q36.2-36.3(chr7:152860576-159325876)x1",
"gene": "BLACE",
"mean_phylop": 0.434,
"track": "phyloP100way"
} | 1 |
co_cons_00014 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_023110.3(FGFR1):c.979_983del (p.His327fs) (in gene FGFR1), classify the evolutionary constraint across the variant's genomic window. | NM_023110.3(FGFR1):c.979_983del (p.His327fs) VARIANT_IN_GENE FGFR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_023110.3(FGFR1):c.979_983del (p.His327fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_023110.3(FGFR1):c.979_983del (p.His327fs)",
"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_023110.3(FGFR1):c.979_983del (p.His327fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 38421895,
"track": "phyloP100way",
"window": 20,
"scores": [
7.80898,
... | [
{
"source_db": "ClinVar",
"source_id": "FGFR1",
"text": "NM_023110.3(FGFR1):c.979_983del (p.His327fs) VARIANT_IN_GENE FGFR1",
"confidence": 1
}
] | {
"variant": "NM_023110.3(FGFR1):c.979_983del (p.His327fs)",
"gene": "FGFR1",
"mean_phylop": 4.816,
"track": "phyloP100way"
} | 1 |
co_cons_00015 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 8q24.12-24.3(chr8:122193546-146295771)x3 (in gene ADCK5), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 8q24.12-24.3(chr8:122193546-146295771)x3 VARIANT_IN_GENE ADCK5 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 8q24.12-24.3(chr8:122193546-146295771)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 8q24.12-24.3(chr8:122193546-146295771)x3",
"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 8q24.12-24.3(chr8:122193546-146295771)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 122193546,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.251... | [
{
"source_db": "ClinVar",
"source_id": "ADCK5",
"text": "GRCh37/hg19 8q24.12-24.3(chr8:122193546-146295771)x3 VARIANT_IN_GENE ADCK5",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 8q24.12-24.3(chr8:122193546-146295771)x3",
"gene": "ADCK5",
"mean_phylop": 0.177,
"track": "phyloP100way"
} | 1 |
co_cons_00016 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004333.6(BRAF):c.1799_1810delinsATG (p.Val600_Trp604delinsAspGly) (in gene BRAF), classify the evolutionary constraint across the variant's genomic window. | NM_004333.6(BRAF):c.1799_1810delinsATG (p.Val600_Trp604delinsAspGly) VARIANT_IN_GENE BRAF | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004333.6(BRAF):c.1799_1810delinsATG (p.Val600_Trp604delinsAspGly)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004333.6(BRAF):c.1799_1810delinsATG (p.Val600_Trp604delinsAspGly)",
"edge_relation": "VARIANT_IN_GENE",
"ed... | 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_004333.6(BRAF):c.1799_1810delinsATG (p.Val600_Trp604delinsAspGly)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 140753325,
"track": "phyloP100way",
"window": 20,
"scores": ... | [
{
"source_db": "ClinVar",
"source_id": "BRAF",
"text": "NM_004333.6(BRAF):c.1799_1810delinsATG (p.Val600_Trp604delinsAspGly) VARIANT_IN_GENE BRAF",
"confidence": 1
}
] | {
"variant": "NM_004333.6(BRAF):c.1799_1810delinsATG (p.Val600_Trp604delinsAspGly)",
"gene": "BRAF",
"mean_phylop": 6.082,
"track": "phyloP100way"
} | 1 |
co_cons_00017 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_002087.4(GRN):c.709-3C>G (in gene LOC125177489), classify the evolutionary constraint across the variant's genomic window. | NM_002087.4(GRN):c.709-3C>G VARIANT_IN_GENE LOC125177489 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002087.4(GRN):c.709-3C>G",
"source_node_type": "VARIANT",
"source_node_label": "NM_002087.4(GRN):c.709-3C>G",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": ... | 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": "NM_002087.4(GRN):c.709-3C>G",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 44351034,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0548189,
-0.358968,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC125177489",
"text": "NM_002087.4(GRN):c.709-3C>G VARIANT_IN_GENE LOC125177489",
"confidence": 1
}
] | {
"variant": "NM_002087.4(GRN):c.709-3C>G",
"gene": "LOC125177489",
"mean_phylop": 1.017,
"track": "phyloP100way"
} | 1 |
co_cons_00018 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 16q23.2-24.3(chr16:80717291-90096662)x3 (in gene ACSF3), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 16q23.2-24.3(chr16:80717291-90096662)x3 VARIANT_IN_GENE ACSF3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 16q23.2-24.3(chr16:80717291-90096662)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 16q23.2-24.3(chr16:80717291-90096662)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 16q23.2-24.3(chr16:80717291-90096662)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 80717291,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0569... | [
{
"source_db": "ClinVar",
"source_id": "ACSF3",
"text": "GRCh38/hg38 16q23.2-24.3(chr16:80717291-90096662)x3 VARIANT_IN_GENE ACSF3",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 16q23.2-24.3(chr16:80717291-90096662)x3",
"gene": "ACSF3",
"mean_phylop": -0.023,
"track": "phyloP100way"
} | 1 |
co_cons_00019 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_015046.7(SETX):c.6838_6841del (p.Asn2280fs) (in gene SETX), classify the evolutionary constraint across the variant's genomic window. | NM_015046.7(SETX):c.6838_6841del (p.Asn2280fs) VARIANT_IN_GENE SETX | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_015046.7(SETX):c.6838_6841del (p.Asn2280fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_015046.7(SETX):c.6838_6841del (p.Asn2280fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | 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_015046.7(SETX):c.6838_6841del (p.Asn2280fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 132278071,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.569960999... | [
{
"source_db": "ClinVar",
"source_id": "SETX",
"text": "NM_015046.7(SETX):c.6838_6841del (p.Asn2280fs) VARIANT_IN_GENE SETX",
"confidence": 1
}
] | {
"variant": "NM_015046.7(SETX):c.6838_6841del (p.Asn2280fs)",
"gene": "SETX",
"mean_phylop": 1.278,
"track": "phyloP100way"
} | 1 |
co_cons_00020 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001291415.2(KDM6A):c.2802_2803dup (p.Pro935fs) (in gene KDM6A), classify the evolutionary constraint across the variant's genomic window. | NM_001291415.2(KDM6A):c.2802_2803dup (p.Pro935fs) VARIANT_IN_GENE KDM6A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001291415.2(KDM6A):c.2802_2803dup (p.Pro935fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001291415.2(KDM6A):c.2802_2803dup (p.Pro935fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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_001291415.2(KDM6A):c.2802_2803dup (p.Pro935fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 45070300,
"track": "phyloP100way",
"window": 20,
"scores": [
3.70983,
... | [
{
"source_db": "ClinVar",
"source_id": "KDM6A",
"text": "NM_001291415.2(KDM6A):c.2802_2803dup (p.Pro935fs) VARIANT_IN_GENE KDM6A",
"confidence": 1
}
] | {
"variant": "NM_001291415.2(KDM6A):c.2802_2803dup (p.Pro935fs)",
"gene": "KDM6A",
"mean_phylop": 3.8449999999999998,
"track": "phyloP100way"
} | 1 |
co_cons_00021 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000477.7(ALB):c.724C>A (p.Arg242Ser) (in gene ALB), classify the evolutionary constraint across the variant's genomic window. | NM_000477.7(ALB):c.724C>A (p.Arg242Ser) VARIANT_IN_GENE ALB | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000477.7(ALB):c.724C>A (p.Arg242Ser)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000477.7(ALB):c.724C>A (p.Arg242Ser)",
"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_000477.7(ALB):c.724C>A (p.Arg242Ser)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 73412006,
"track": "phyloP100way",
"window": 20,
"scores": [
0.974173,
0.... | [
{
"source_db": "ClinVar",
"source_id": "ALB",
"text": "NM_000477.7(ALB):c.724C>A (p.Arg242Ser) VARIANT_IN_GENE ALB",
"confidence": 1
}
] | {
"variant": "NM_000477.7(ALB):c.724C>A (p.Arg242Ser)",
"gene": "ALB",
"mean_phylop": 1.09,
"track": "phyloP100way"
} | 1 |
co_cons_00022 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000535.7(PMS2):c.2516_2519del (p.His839fs) (in gene PMS2), classify the evolutionary constraint across the variant's genomic window. | NM_000535.7(PMS2):c.2516_2519del (p.His839fs) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.2516_2519del (p.His839fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.2516_2519del (p.His839fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | 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_000535.7(PMS2):c.2516_2519del (p.His839fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 5973469,
"track": "phyloP100way",
"window": 20,
"scores": [
1.59625,
... | [
{
"source_db": "ClinVar",
"source_id": "PMS2",
"text": "NM_000535.7(PMS2):c.2516_2519del (p.His839fs) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.2516_2519del (p.His839fs)",
"gene": "PMS2",
"mean_phylop": 5.893,
"track": "phyloP100way"
} | 1 |
co_cons_00023 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 10q25.3-26.13(chr10:117019650-125217066) (in gene ACADSB), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 10q25.3-26.13(chr10:117019650-125217066) VARIANT_IN_GENE ACADSB | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 10q25.3-26.13(chr10:117019650-125217066)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 10q25.3-26.13(chr10:117019650-125217066)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | 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": "GRCh37/hg19 10q25.3-26.13(chr10:117019650-125217066)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 117019650,
"track": "phyloP100way",
"window": 20,
"scores": [
0.180... | [
{
"source_db": "ClinVar",
"source_id": "ACADSB",
"text": "GRCh37/hg19 10q25.3-26.13(chr10:117019650-125217066) VARIANT_IN_GENE ACADSB",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 10q25.3-26.13(chr10:117019650-125217066)",
"gene": "ACADSB",
"mean_phylop": 0.096,
"track": "phyloP100way"
} | 1 |
co_cons_00024 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004448.4(ERBB2):c.2740G>A (p.Glu914Lys) (in gene ERBB2), classify the evolutionary constraint across the variant's genomic window. | NM_004448.4(ERBB2):c.2740G>A (p.Glu914Lys) VARIANT_IN_GENE ERBB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004448.4(ERBB2):c.2740G>A (p.Glu914Lys)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004448.4(ERBB2):c.2740G>A (p.Glu914Lys)",
"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_004448.4(ERBB2):c.2740G>A (p.Glu914Lys)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 39725721,
"track": "phyloP100way",
"window": 20,
"scores": [
0.176709,
... | [
{
"source_db": "ClinVar",
"source_id": "ERBB2",
"text": "NM_004448.4(ERBB2):c.2740G>A (p.Glu914Lys) VARIANT_IN_GENE ERBB2",
"confidence": 1
}
] | {
"variant": "NM_004448.4(ERBB2):c.2740G>A (p.Glu914Lys)",
"gene": "ERBB2",
"mean_phylop": 5.524,
"track": "phyloP100way"
} | 1 |
co_cons_00025 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 3q13.2-13.31(chr3:112425234-115795585)x1 (in gene ATG3), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 3q13.2-13.31(chr3:112425234-115795585)x1 VARIANT_IN_GENE ATG3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 3q13.2-13.31(chr3:112425234-115795585)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 3q13.2-13.31(chr3:112425234-115795585)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 3q13.2-13.31(chr3:112425234-115795585)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 112425234,
"track": "phyloP100way",
"window": 20,
"scores": [
0.3556... | [
{
"source_db": "ClinVar",
"source_id": "ATG3",
"text": "GRCh38/hg38 3q13.2-13.31(chr3:112425234-115795585)x1 VARIANT_IN_GENE ATG3",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 3q13.2-13.31(chr3:112425234-115795585)x1",
"gene": "ATG3",
"mean_phylop": 0.074,
"track": "phyloP100way"
} | 1 |
co_cons_00026 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1 (in gene LOC129993405), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1 VARIANT_IN_GENE LOC129993405 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)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": "GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 167373716,
"track": "phyloP100way",
"window": 20,
"scores": [
1.32374... | [
{
"source_db": "ClinVar",
"source_id": "LOC129993405",
"text": "GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1 VARIANT_IN_GENE LOC129993405",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 4q32.3-35.2(chr4:167373716-190036318)x1",
"gene": "LOC129993405",
"mean_phylop": -0.095,
"track": "phyloP100way"
} | 1 |
co_cons_00027 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_012179.4(FBXO7):c.1144+1G>T (in gene FBXO7), classify the evolutionary constraint across the variant's genomic window. | NM_012179.4(FBXO7):c.1144+1G>T VARIANT_IN_GENE FBXO7 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_012179.4(FBXO7):c.1144+1G>T",
"source_node_type": "VARIANT",
"source_node_label": "NM_012179.4(FBXO7):c.1144+1G>T",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source... | 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_012179.4(FBXO7):c.1144+1G>T",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 32493282,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.128465,
4.46169,
... | [
{
"source_db": "ClinVar",
"source_id": "FBXO7",
"text": "NM_012179.4(FBXO7):c.1144+1G>T VARIANT_IN_GENE FBXO7",
"confidence": 1
}
] | {
"variant": "NM_012179.4(FBXO7):c.1144+1G>T",
"gene": "FBXO7",
"mean_phylop": 1.99,
"track": "phyloP100way"
} | 1 |
co_cons_00028 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 8p11.23-11.21(chr8:38065927-40341650)x1 (in gene ADAM18), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 8p11.23-11.21(chr8:38065927-40341650)x1 VARIANT_IN_GENE ADAM18 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 8p11.23-11.21(chr8:38065927-40341650)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 8p11.23-11.21(chr8:38065927-40341650)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 8p11.23-11.21(chr8:38065927-40341650)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 38065927,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.60695... | [
{
"source_db": "ClinVar",
"source_id": "ADAM18",
"text": "GRCh38/hg38 8p11.23-11.21(chr8:38065927-40341650)x1 VARIANT_IN_GENE ADAM18",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 8p11.23-11.21(chr8:38065927-40341650)x1",
"gene": "ADAM18",
"mean_phylop": -0.043000000000000003,
"track": "phyloP100way"
} | 1 |
co_cons_00029 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 21q22.3(chr21:44310057-47503155)x1 (in gene ADARB1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 21q22.3(chr21:44310057-47503155)x1 VARIANT_IN_GENE ADARB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 21q22.3(chr21:44310057-47503155)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 21q22.3(chr21:44310057-47503155)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | 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 21q22.3(chr21:44310057-47503155)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 44310057,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.952803,
... | [
{
"source_db": "ClinVar",
"source_id": "ADARB1",
"text": "GRCh37/hg19 21q22.3(chr21:44310057-47503155)x1 VARIANT_IN_GENE ADARB1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 21q22.3(chr21:44310057-47503155)x1",
"gene": "ADARB1",
"mean_phylop": -0.838,
"track": "phyloP100way"
} | 1 |
co_cons_00030 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3 (in gene LOC130009717), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3 VARIANT_IN_GENE LOC130009717 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | 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": "GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr13",
"pos": 18456040,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.218409,... | [
{
"source_db": "ClinVar",
"source_id": "LOC130009717",
"text": "GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3 VARIANT_IN_GENE LOC130009717",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3",
"gene": "LOC130009717",
"mean_phylop": -0.158,
"track": "phyloP100way"
} | 1 |
co_cons_00031 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 4q13.3-22.1(chr4:75737340-91131156) (in gene ABCG2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 4q13.3-22.1(chr4:75737340-91131156) VARIANT_IN_GENE ABCG2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 4q13.3-22.1(chr4:75737340-91131156)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 4q13.3-22.1(chr4:75737340-91131156)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | 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 4q13.3-22.1(chr4:75737340-91131156)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 75737340,
"track": "phyloP100way",
"window": 20,
"scores": [
0.956465,
... | [
{
"source_db": "ClinVar",
"source_id": "ABCG2",
"text": "GRCh37/hg19 4q13.3-22.1(chr4:75737340-91131156) VARIANT_IN_GENE ABCG2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 4q13.3-22.1(chr4:75737340-91131156)",
"gene": "ABCG2",
"mean_phylop": 0.07100000000000001,
"track": "phyloP100way"
} | 1 |
co_cons_00032 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_012120.3(CD2AP):c.494del (p.Glu164_Leu165insTer) (in gene CD2AP), classify the evolutionary constraint across the variant's genomic window. | NM_012120.3(CD2AP):c.494del (p.Glu164_Leu165insTer) VARIANT_IN_GENE CD2AP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_012120.3(CD2AP):c.494del (p.Glu164_Leu165insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_012120.3(CD2AP):c.494del (p.Glu164_Leu165insTer)",
"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_012120.3(CD2AP):c.494del (p.Glu164_Leu165insTer)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 47554718,
"track": "phyloP100way",
"window": 20,
"scores": [
7.18551,... | [
{
"source_db": "ClinVar",
"source_id": "CD2AP",
"text": "NM_012120.3(CD2AP):c.494del (p.Glu164_Leu165insTer) VARIANT_IN_GENE CD2AP",
"confidence": 1
}
] | {
"variant": "NM_012120.3(CD2AP):c.494del (p.Glu164_Leu165insTer)",
"gene": "CD2AP",
"mean_phylop": 3.653,
"track": "phyloP100way"
} | 1 |
co_cons_00033 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004960.4(FUS):c.1526G>A (p.Gly509Asp) (in gene FUS), classify the evolutionary constraint across the variant's genomic window. | NM_004960.4(FUS):c.1526G>A (p.Gly509Asp) VARIANT_IN_GENE FUS | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004960.4(FUS):c.1526G>A (p.Gly509Asp)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004960.4(FUS):c.1526G>A (p.Gly509Asp)",
"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_004960.4(FUS):c.1526G>A (p.Gly509Asp)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 31191095,
"track": "phyloP100way",
"window": 20,
"scores": [
0.129528,
... | [
{
"source_db": "ClinVar",
"source_id": "FUS",
"text": "NM_004960.4(FUS):c.1526G>A (p.Gly509Asp) VARIANT_IN_GENE FUS",
"confidence": 1
}
] | {
"variant": "NM_004960.4(FUS):c.1526G>A (p.Gly509Asp)",
"gene": "FUS",
"mean_phylop": 4.027,
"track": "phyloP100way"
} | 1 |
co_cons_00034 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 18q21.1-23(chr18:47656799-78014123) (in gene ALPK2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 18q21.1-23(chr18:47656799-78014123) VARIANT_IN_GENE ALPK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 18q21.1-23(chr18:47656799-78014123)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 18q21.1-23(chr18:47656799-78014123)",
"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"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 18q21.1-23(chr18:47656799-78014123)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr18",
"pos": 47656799,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0845433,
... | [
{
"source_db": "ClinVar",
"source_id": "ALPK2",
"text": "GRCh37/hg19 18q21.1-23(chr18:47656799-78014123) VARIANT_IN_GENE ALPK2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 18q21.1-23(chr18:47656799-78014123)",
"gene": "ALPK2",
"mean_phylop": 0.123,
"track": "phyloP100way"
} | 1 |
co_cons_00035 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001042492.3(NF1):c.5268+5G>T (in gene EVI2A), classify the evolutionary constraint across the variant's genomic window. | NM_001042492.3(NF1):c.5268+5G>T VARIANT_IN_GENE EVI2A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001042492.3(NF1):c.5268+5G>T",
"source_node_type": "VARIANT",
"source_node_label": "NM_001042492.3(NF1):c.5268+5G>T",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_sour... | 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": "NM_001042492.3(NF1):c.5268+5G>T",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 31326257,
"track": "phyloP100way",
"window": 20,
"scores": [
5.63717,
8.80045,
... | [
{
"source_db": "ClinVar",
"source_id": "EVI2A",
"text": "NM_001042492.3(NF1):c.5268+5G>T VARIANT_IN_GENE EVI2A",
"confidence": 1
}
] | {
"variant": "NM_001042492.3(NF1):c.5268+5G>T",
"gene": "EVI2A",
"mean_phylop": 2.7,
"track": "phyloP100way"
} | 1 |
co_cons_00036 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001211.6(BUB1B):c.578del (p.His193fs) (in gene BUB1B), classify the evolutionary constraint across the variant's genomic window. | NM_001211.6(BUB1B):c.578del (p.His193fs) VARIANT_IN_GENE BUB1B | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001211.6(BUB1B):c.578del (p.His193fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001211.6(BUB1B):c.578del (p.His193fs)",
"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_001211.6(BUB1B):c.578del (p.His193fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr15",
"pos": 40176670,
"track": "phyloP100way",
"window": 20,
"scores": [
0.4197479999999999... | [
{
"source_db": "ClinVar",
"source_id": "BUB1B",
"text": "NM_001211.6(BUB1B):c.578del (p.His193fs) VARIANT_IN_GENE BUB1B",
"confidence": 1
}
] | {
"variant": "NM_001211.6(BUB1B):c.578del (p.His193fs)",
"gene": "BUB1B",
"mean_phylop": 2.6630000000000003,
"track": "phyloP100way"
} | 1 |
co_cons_00037 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 3q26.33-27.2(chr3:181062175-185474509)x1 (in gene ABCC5), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 3q26.33-27.2(chr3:181062175-185474509)x1 VARIANT_IN_GENE ABCC5 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 3q26.33-27.2(chr3:181062175-185474509)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 3q26.33-27.2(chr3:181062175-185474509)x1",
"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 3q26.33-27.2(chr3:181062175-185474509)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 181062175,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.529... | [
{
"source_db": "ClinVar",
"source_id": "ABCC5",
"text": "GRCh37/hg19 3q26.33-27.2(chr3:181062175-185474509)x1 VARIANT_IN_GENE ABCC5",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 3q26.33-27.2(chr3:181062175-185474509)x1",
"gene": "ABCC5",
"mean_phylop": 0.222,
"track": "phyloP100way"
} | 1 |
co_cons_00038 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985) (in gene LOC105377134), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985) VARIANT_IN_GENE LOC105377134 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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": "GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 13974874,
"track": "phyloP100way",
"window": 20,
"scores": [
2.00467,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC105377134",
"text": "GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985) VARIANT_IN_GENE LOC105377134",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 21q11.2-21.3(chr21:14000146-27785985)",
"gene": "LOC105377134",
"mean_phylop": 0.248,
"track": "phyloP100way"
} | 1 |
co_cons_00039 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000003.11:g.(?_37034289)_(37092144_?)del (in gene EPM2AIP1), classify the evolutionary constraint across the variant's genomic window. | NC_000003.11:g.(?_37034289)_(37092144_?)del VARIANT_IN_GENE EPM2AIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000003.11:g.(?_37034289)_(37092144_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000003.11:g.(?_37034289)_(37092144_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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": "NC_000003.11:g.(?_37034289)_(37092144_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 37034289,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.76529,
... | [
{
"source_db": "ClinVar",
"source_id": "EPM2AIP1",
"text": "NC_000003.11:g.(?_37034289)_(37092144_?)del VARIANT_IN_GENE EPM2AIP1",
"confidence": 1
}
] | {
"variant": "NC_000003.11:g.(?_37034289)_(37092144_?)del",
"gene": "EPM2AIP1",
"mean_phylop": 0.152,
"track": "phyloP100way"
} | 1 |
co_cons_00040 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3 (in gene CCDC116), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3 VARIANT_IN_GENE CCDC116 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3",
"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"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 21923858,
"track": "phyloP100way",
"window": 20,
"scores": [
0.110... | [
{
"source_db": "ClinVar",
"source_id": "CCDC116",
"text": "GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3 VARIANT_IN_GENE CCDC116",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 22q11.21-11.22(chr22:21923858-23025727)x3",
"gene": "CCDC116",
"mean_phylop": -0.03,
"track": "phyloP100way"
} | 1 |
co_cons_00041 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3 (in gene LOC112694698), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3 VARIANT_IN_GENE LOC112694698 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3",
"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 20p13-11.21(chr20:87153-23635465)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 87153,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.420661,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC112694698",
"text": "GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3 VARIANT_IN_GENE LOC112694698",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3",
"gene": "LOC112694698",
"mean_phylop": 0.12,
"track": "phyloP100way"
} | 1 |
co_cons_00042 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_002524.5(NRAS):c.108A>G (p.Ile36Met) (in gene NRAS), classify the evolutionary constraint across the variant's genomic window. | NM_002524.5(NRAS):c.108A>G (p.Ile36Met) VARIANT_IN_GENE NRAS | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002524.5(NRAS):c.108A>G (p.Ile36Met)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002524.5(NRAS):c.108A>G (p.Ile36Met)",
"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_002524.5(NRAS):c.108A>G (p.Ile36Met)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 114716053,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.613945,
... | [
{
"source_db": "ClinVar",
"source_id": "NRAS",
"text": "NM_002524.5(NRAS):c.108A>G (p.Ile36Met) VARIANT_IN_GENE NRAS",
"confidence": 1
}
] | {
"variant": "NM_002524.5(NRAS):c.108A>G (p.Ile36Met)",
"gene": "NRAS",
"mean_phylop": 4.289,
"track": "phyloP100way"
} | 1 |
co_cons_00043 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000010.10:g.(?_81697608)_(82049179_?)del (in gene ANXA11), classify the evolutionary constraint across the variant's genomic window. | NC_000010.10:g.(?_81697608)_(82049179_?)del VARIANT_IN_GENE ANXA11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000010.10:g.(?_81697608)_(82049179_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000010.10:g.(?_81697608)_(82049179_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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": "NC_000010.10:g.(?_81697608)_(82049179_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 81697608,
"track": "phyloP100way",
"window": 20,
"scores": [
0.227102,
... | [
{
"source_db": "ClinVar",
"source_id": "ANXA11",
"text": "NC_000010.10:g.(?_81697608)_(82049179_?)del VARIANT_IN_GENE ANXA11",
"confidence": 1
}
] | {
"variant": "NC_000010.10:g.(?_81697608)_(82049179_?)del",
"gene": "ANXA11",
"mean_phylop": 0.083,
"track": "phyloP100way"
} | 1 |
co_cons_00044 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 4p16.3-16.1(chr4:51519-8222798)x3 (in gene LOC126806941), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 4p16.3-16.1(chr4:51519-8222798)x3 VARIANT_IN_GENE LOC126806941 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 4p16.3-16.1(chr4:51519-8222798)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 4p16.3-16.1(chr4:51519-8222798)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | 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 4p16.3-16.1(chr4:51519-8222798)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 51519,
"track": "phyloP100way",
"window": 20,
"scores": [
0.251542999999999... | [
{
"source_db": "ClinVar",
"source_id": "LOC126806941",
"text": "GRCh38/hg38 4p16.3-16.1(chr4:51519-8222798)x3 VARIANT_IN_GENE LOC126806941",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 4p16.3-16.1(chr4:51519-8222798)x3",
"gene": "LOC126806941",
"mean_phylop": 0.179,
"track": "phyloP100way"
} | 1 |
co_cons_00045 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 6q27(chr6:167924952-170602152)x1 (in gene AFDN), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 6q27(chr6:167924952-170602152)x1 VARIANT_IN_GENE AFDN | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 6q27(chr6:167924952-170602152)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 6q27(chr6:167924952-170602152)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | 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",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 6q27(chr6:167924952-170602152)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 167924952,
"track": "phyloP100way",
"window": 20,
"scores": [
-3.01455,
... | [
{
"source_db": "ClinVar",
"source_id": "AFDN",
"text": "GRCh38/hg38 6q27(chr6:167924952-170602152)x1 VARIANT_IN_GENE AFDN",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 6q27(chr6:167924952-170602152)x1",
"gene": "AFDN",
"mean_phylop": -0.625,
"track": "phyloP100way"
} | 1 |
co_cons_00046 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_032043.3(BRIP1):c.128dup (p.Leu43fs) (in gene BRIP1), classify the evolutionary constraint across the variant's genomic window. | NM_032043.3(BRIP1):c.128dup (p.Leu43fs) VARIANT_IN_GENE BRIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032043.3(BRIP1):c.128dup (p.Leu43fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032043.3(BRIP1):c.128dup (p.Leu43fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | 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_032043.3(BRIP1):c.128dup (p.Leu43fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 61859872,
"track": "phyloP100way",
"window": 20,
"scores": [
6.66988,
6.... | [
{
"source_db": "ClinVar",
"source_id": "BRIP1",
"text": "NM_032043.3(BRIP1):c.128dup (p.Leu43fs) VARIANT_IN_GENE BRIP1",
"confidence": 1
}
] | {
"variant": "NM_032043.3(BRIP1):c.128dup (p.Leu43fs)",
"gene": "BRIP1",
"mean_phylop": 4.307,
"track": "phyloP100way"
} | 1 |
co_cons_00047 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000251.3(MSH2):c.2310dup (p.Ala771fs) (in gene MSH2), classify the evolutionary constraint across the variant's genomic window. | NM_000251.3(MSH2):c.2310dup (p.Ala771fs) VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000251.3(MSH2):c.2310dup (p.Ala771fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000251.3(MSH2):c.2310dup (p.Ala771fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | 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_000251.3(MSH2):c.2310dup (p.Ala771fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 47478369,
"track": "phyloP100way",
"window": 20,
"scores": [
7.44994,
-2... | [
{
"source_db": "ClinVar",
"source_id": "MSH2",
"text": "NM_000251.3(MSH2):c.2310dup (p.Ala771fs) VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NM_000251.3(MSH2):c.2310dup (p.Ala771fs)",
"gene": "MSH2",
"mean_phylop": 4.193,
"track": "phyloP100way"
} | 1 |
co_cons_00048 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 5q35.2-35.3(chr5:176497464-177776599)x3 (in gene B4GALT7), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 5q35.2-35.3(chr5:176497464-177776599)x3 VARIANT_IN_GENE B4GALT7 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 5q35.2-35.3(chr5:176497464-177776599)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 5q35.2-35.3(chr5:176497464-177776599)x3",
"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"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 5q35.2-35.3(chr5:176497464-177776599)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 176497464,
"track": "phyloP100way",
"window": 20,
"scores": [
1.06446... | [
{
"source_db": "ClinVar",
"source_id": "B4GALT7",
"text": "GRCh37/hg19 5q35.2-35.3(chr5:176497464-177776599)x3 VARIANT_IN_GENE B4GALT7",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 5q35.2-35.3(chr5:176497464-177776599)x3",
"gene": "B4GALT7",
"mean_phylop": -0.018000000000000002,
"track": "phyloP100way"
} | 1 |
co_cons_00049 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000251.3(MSH2):c.280_281insG (p.Leu94fs) (in gene MSH2), classify the evolutionary constraint across the variant's genomic window. | NM_000251.3(MSH2):c.280_281insG (p.Leu94fs) VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000251.3(MSH2):c.280_281insG (p.Leu94fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000251.3(MSH2):c.280_281insG (p.Leu94fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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_000251.3(MSH2):c.280_281insG (p.Leu94fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 47408469,
"track": "phyloP100way",
"window": 20,
"scores": [
5.00014,
... | [
{
"source_db": "ClinVar",
"source_id": "MSH2",
"text": "NM_000251.3(MSH2):c.280_281insG (p.Leu94fs) VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NM_000251.3(MSH2):c.280_281insG (p.Leu94fs)",
"gene": "MSH2",
"mean_phylop": 3.976,
"track": "phyloP100way"
} | 1 |
co_cons_00050 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 11p14.3-14.1(chr11:23024064-27978597)x1 (in gene ANO3), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 11p14.3-14.1(chr11:23024064-27978597)x1 VARIANT_IN_GENE ANO3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 11p14.3-14.1(chr11:23024064-27978597)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 11p14.3-14.1(chr11:23024064-27978597)x1",
"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 11p14.3-14.1(chr11:23024064-27978597)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr11",
"pos": 23024064,
"track": "phyloP100way",
"window": 20,
"scores": [
0.55796... | [
{
"source_db": "ClinVar",
"source_id": "ANO3",
"text": "GRCh38/hg38 11p14.3-14.1(chr11:23024064-27978597)x1 VARIANT_IN_GENE ANO3",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 11p14.3-14.1(chr11:23024064-27978597)x1",
"gene": "ANO3",
"mean_phylop": 0.075,
"track": "phyloP100way"
} | 1 |
co_cons_00051 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter) (in gene BUB1B), classify the evolutionary constraint across the variant's genomic window. | NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter) VARIANT_IN_GENE BUB1B | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"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_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr15",
"pos": 40185338,
"track": "phyloP100way",
"window": 20,
"scores": [
3.36161,
... | [
{
"source_db": "ClinVar",
"source_id": "BUB1B",
"text": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter) VARIANT_IN_GENE BUB1B",
"confidence": 1
}
] | {
"variant": "NM_001211.6(BUB1B):c.925C>T (p.Gln309Ter)",
"gene": "BUB1B",
"mean_phylop": 3.061,
"track": "phyloP100way"
} | 1 |
co_cons_00052 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000535.7(PMS2):c.700A>T (p.Lys234Ter) (in gene PMS2), classify the evolutionary constraint across the variant's genomic window. | NM_000535.7(PMS2):c.700A>T (p.Lys234Ter) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.700A>T (p.Lys234Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.700A>T (p.Lys234Ter)",
"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_000535.7(PMS2):c.700A>T (p.Lys234Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 5999113,
"track": "phyloP100way",
"window": 20,
"scores": [
0.913654,
0.... | [
{
"source_db": "ClinVar",
"source_id": "PMS2",
"text": "NM_000535.7(PMS2):c.700A>T (p.Lys234Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.700A>T (p.Lys234Ter)",
"gene": "PMS2",
"mean_phylop": 3.684,
"track": "phyloP100way"
} | 1 |
co_cons_00053 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 11p15.1-13(chr11:21586131-33168232)x1 (in gene ANO3), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 11p15.1-13(chr11:21586131-33168232)x1 VARIANT_IN_GENE ANO3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 11p15.1-13(chr11:21586131-33168232)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 11p15.1-13(chr11:21586131-33168232)x1",
"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 11p15.1-13(chr11:21586131-33168232)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr11",
"pos": 21586131,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.01651,... | [
{
"source_db": "ClinVar",
"source_id": "ANO3",
"text": "GRCh37/hg19 11p15.1-13(chr11:21586131-33168232)x1 VARIANT_IN_GENE ANO3",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 11p15.1-13(chr11:21586131-33168232)x1",
"gene": "ANO3",
"mean_phylop": -0.018000000000000002,
"track": "phyloP100way"
} | 1 |
co_cons_00054 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_017617.5(NOTCH1):c.4120T>C (p.Cys1374Arg) (in gene NOTCH1), classify the evolutionary constraint across the variant's genomic window. | NM_017617.5(NOTCH1):c.4120T>C (p.Cys1374Arg) VARIANT_IN_GENE NOTCH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_017617.5(NOTCH1):c.4120T>C (p.Cys1374Arg)",
"source_node_type": "VARIANT",
"source_node_label": "NM_017617.5(NOTCH1):c.4120T>C (p.Cys1374Arg)",
"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_017617.5(NOTCH1):c.4120T>C (p.Cys1374Arg)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 136505776,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0405984,
... | [
{
"source_db": "ClinVar",
"source_id": "NOTCH1",
"text": "NM_017617.5(NOTCH1):c.4120T>C (p.Cys1374Arg) VARIANT_IN_GENE NOTCH1",
"confidence": 1
}
] | {
"variant": "NM_017617.5(NOTCH1):c.4120T>C (p.Cys1374Arg)",
"gene": "NOTCH1",
"mean_phylop": 3.132,
"track": "phyloP100way"
} | 1 |
co_cons_00055 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 14q24.3-31.1(chr14:75489052-79610332)x1 (in gene LOC130056176), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 14q24.3-31.1(chr14:75489052-79610332)x1 VARIANT_IN_GENE LOC130056176 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 14q24.3-31.1(chr14:75489052-79610332)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 14q24.3-31.1(chr14:75489052-79610332)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"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 14q24.3-31.1(chr14:75489052-79610332)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 75489052,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.2784... | [
{
"source_db": "ClinVar",
"source_id": "LOC130056176",
"text": "GRCh38/hg38 14q24.3-31.1(chr14:75489052-79610332)x1 VARIANT_IN_GENE LOC130056176",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 14q24.3-31.1(chr14:75489052-79610332)x1",
"gene": "LOC130056176",
"mean_phylop": -0.134,
"track": "phyloP100way"
} | 1 |
co_cons_00056 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004960.4(FUS):c.1571G>T (p.Arg524Met) (in gene FUS), classify the evolutionary constraint across the variant's genomic window. | NM_004960.4(FUS):c.1571G>T (p.Arg524Met) VARIANT_IN_GENE FUS | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004960.4(FUS):c.1571G>T (p.Arg524Met)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004960.4(FUS):c.1571G>T (p.Arg524Met)",
"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_004960.4(FUS):c.1571G>T (p.Arg524Met)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 31191428,
"track": "phyloP100way",
"window": 20,
"scores": [
3.74402,
3... | [
{
"source_db": "ClinVar",
"source_id": "FUS",
"text": "NM_004960.4(FUS):c.1571G>T (p.Arg524Met) VARIANT_IN_GENE FUS",
"confidence": 1
}
] | {
"variant": "NM_004960.4(FUS):c.1571G>T (p.Arg524Met)",
"gene": "FUS",
"mean_phylop": 2.729,
"track": "phyloP100way"
} | 1 |
co_cons_00057 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 3q26.33(chr3:179016729-181527320)x1 (in gene ACTL6A), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 3q26.33(chr3:179016729-181527320)x1 VARIANT_IN_GENE ACTL6A | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 3q26.33(chr3:179016729-181527320)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 3q26.33(chr3:179016729-181527320)x1",
"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 3q26.33(chr3:179016729-181527320)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 179016729,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.637386,
... | [
{
"source_db": "ClinVar",
"source_id": "ACTL6A",
"text": "GRCh37/hg19 3q26.33(chr3:179016729-181527320)x1 VARIANT_IN_GENE ACTL6A",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 3q26.33(chr3:179016729-181527320)x1",
"gene": "ACTL6A",
"mean_phylop": 0.38,
"track": "phyloP100way"
} | 1 |
co_cons_00058 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 16p13.3-13.13(chr16:85880-11209288)x3 (in gene PDPK1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 16p13.3-13.13(chr16:85880-11209288)x3 VARIANT_IN_GENE PDPK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 16p13.3-13.13(chr16:85880-11209288)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 16p13.3-13.13(chr16:85880-11209288)x3",
"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 16p13.3-13.13(chr16:85880-11209288)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 85880,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.617748,
... | [
{
"source_db": "ClinVar",
"source_id": "PDPK1",
"text": "GRCh37/hg19 16p13.3-13.13(chr16:85880-11209288)x3 VARIANT_IN_GENE PDPK1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 16p13.3-13.13(chr16:85880-11209288)x3",
"gene": "PDPK1",
"mean_phylop": -0.843,
"track": "phyloP100way"
} | 1 |
co_cons_00059 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001008212.2(OPTN):c.235C>T (p.Gln79Ter) (in gene OPTN), classify the evolutionary constraint across the variant's genomic window. | NM_001008212.2(OPTN):c.235C>T (p.Gln79Ter) VARIANT_IN_GENE OPTN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001008212.2(OPTN):c.235C>T (p.Gln79Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001008212.2(OPTN):c.235C>T (p.Gln79Ter)",
"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_001008212.2(OPTN):c.235C>T (p.Gln79Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 13110342,
"track": "phyloP100way",
"window": 20,
"scores": [
5.97635,
... | [
{
"source_db": "ClinVar",
"source_id": "OPTN",
"text": "NM_001008212.2(OPTN):c.235C>T (p.Gln79Ter) VARIANT_IN_GENE OPTN",
"confidence": 1
}
] | {
"variant": "NM_001008212.2(OPTN):c.235C>T (p.Gln79Ter)",
"gene": "OPTN",
"mean_phylop": 3.5540000000000003,
"track": "phyloP100way"
} | 1 |
co_cons_00060 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 7p22.3-21.3(chr7:43360-9649794)x3 (in gene ACTB), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 7p22.3-21.3(chr7:43360-9649794)x3 VARIANT_IN_GENE ACTB | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 7p22.3-21.3(chr7:43360-9649794)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 7p22.3-21.3(chr7:43360-9649794)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | 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",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 7p22.3-21.3(chr7:43360-9649794)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 43360,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0296378,
... | [
{
"source_db": "ClinVar",
"source_id": "ACTB",
"text": "GRCh37/hg19 7p22.3-21.3(chr7:43360-9649794)x3 VARIANT_IN_GENE ACTB",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 7p22.3-21.3(chr7:43360-9649794)x3",
"gene": "ACTB",
"mean_phylop": -0.027,
"track": "phyloP100way"
} | 1 |
co_cons_00061 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_032409.3(PINK1):c.1600C>T (p.Gln534Ter) (in gene PINK1), classify the evolutionary constraint across the variant's genomic window. | NM_032409.3(PINK1):c.1600C>T (p.Gln534Ter) VARIANT_IN_GENE PINK1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_032409.3(PINK1):c.1600C>T (p.Gln534Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_032409.3(PINK1):c.1600C>T (p.Gln534Ter)",
"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_032409.3(PINK1):c.1600C>T (p.Gln534Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 20650545,
"track": "phyloP100way",
"window": 20,
"scores": [
6.2143,
3... | [
{
"source_db": "ClinVar",
"source_id": "PINK1",
"text": "NM_032409.3(PINK1):c.1600C>T (p.Gln534Ter) VARIANT_IN_GENE PINK1",
"confidence": 1
}
] | {
"variant": "NM_032409.3(PINK1):c.1600C>T (p.Gln534Ter)",
"gene": "PINK1",
"mean_phylop": 2.982,
"track": "phyloP100way"
} | 1 |
co_cons_00062 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_005228.5(EGFR):c.2312_2314dup (p.Asn771_Pro772insHis) (in gene EGFR-AS1), classify the evolutionary constraint across the variant's genomic window. | NM_005228.5(EGFR):c.2312_2314dup (p.Asn771_Pro772insHis) VARIANT_IN_GENE EGFR-AS1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_005228.5(EGFR):c.2312_2314dup (p.Asn771_Pro772insHis)",
"source_node_type": "VARIANT",
"source_node_label": "NM_005228.5(EGFR):c.2312_2314dup (p.Asn771_Pro772insHis)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "cura... | 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"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_005228.5(EGFR):c.2312_2314dup (p.Asn771_Pro772insHis)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 55181320,
"track": "phyloP100way",
"window": 20,
"scores": [
9.1... | [
{
"source_db": "ClinVar",
"source_id": "EGFR-AS1",
"text": "NM_005228.5(EGFR):c.2312_2314dup (p.Asn771_Pro772insHis) VARIANT_IN_GENE EGFR-AS1",
"confidence": 1
}
] | {
"variant": "NM_005228.5(EGFR):c.2312_2314dup (p.Asn771_Pro772insHis)",
"gene": "EGFR-AS1",
"mean_phylop": 5.347,
"track": "phyloP100way"
} | 1 |
co_cons_00063 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 1p32.1-31.1(chr1:59760856-71578052)x1 (in gene AK4), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 1p32.1-31.1(chr1:59760856-71578052)x1 VARIANT_IN_GENE AK4 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 1p32.1-31.1(chr1:59760856-71578052)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 1p32.1-31.1(chr1:59760856-71578052)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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 1p32.1-31.1(chr1:59760856-71578052)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 59760856,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.103921,... | [
{
"source_db": "ClinVar",
"source_id": "AK4",
"text": "GRCh38/hg38 1p32.1-31.1(chr1:59760856-71578052)x1 VARIANT_IN_GENE AK4",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 1p32.1-31.1(chr1:59760856-71578052)x1",
"gene": "AK4",
"mean_phylop": -0.138,
"track": "phyloP100way"
} | 1 |
co_cons_00064 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 (in gene ACP6), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 VARIANT_IN_GENE ACP6 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3",
"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 1q21.1-23.1(chr1:144368497-158992086)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 144368497,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0231... | [
{
"source_db": "ClinVar",
"source_id": "ACP6",
"text": "GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 VARIANT_IN_GENE ACP6",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3",
"gene": "ACP6",
"mean_phylop": -0.077,
"track": "phyloP100way"
} | 1 |
co_cons_00065 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_006262.4(PRPH):c.919C>T (p.Gln307Ter) (in gene PRPH), classify the evolutionary constraint across the variant's genomic window. | NM_006262.4(PRPH):c.919C>T (p.Gln307Ter) VARIANT_IN_GENE PRPH | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_006262.4(PRPH):c.919C>T (p.Gln307Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_006262.4(PRPH):c.919C>T (p.Gln307Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | 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_006262.4(PRPH):c.919C>T (p.Gln307Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 49297196,
"track": "phyloP100way",
"window": 20,
"scores": [
3.15396,
0... | [
{
"source_db": "ClinVar",
"source_id": "PRPH",
"text": "NM_006262.4(PRPH):c.919C>T (p.Gln307Ter) VARIANT_IN_GENE PRPH",
"confidence": 1
}
] | {
"variant": "NM_006262.4(PRPH):c.919C>T (p.Gln307Ter)",
"gene": "PRPH",
"mean_phylop": 4.899,
"track": "phyloP100way"
} | 1 |
co_cons_00066 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3 (in gene ANO3), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3 VARIANT_IN_GENE ANO3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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": "GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr11",
"pos": 24595399,
"track": "phyloP100way",
"window": 20,
"scores": [
1.62748,
... | [
{
"source_db": "ClinVar",
"source_id": "ANO3",
"text": "GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3 VARIANT_IN_GENE ANO3",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 11p14.3-13(chr11:24595399-31096539)x3",
"gene": "ANO3",
"mean_phylop": 1.236,
"track": "phyloP100way"
} | 1 |
co_cons_00067 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000012.11:g.(?_132414268)_(133263901_?)del (in gene DDX51), classify the evolutionary constraint across the variant's genomic window. | NC_000012.11:g.(?_132414268)_(133263901_?)del VARIANT_IN_GENE DDX51 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000012.11:g.(?_132414268)_(133263901_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000012.11:g.(?_132414268)_(133263901_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | 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": "NC_000012.11:g.(?_132414268)_(133263901_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 132414268,
"track": "phyloP100way",
"window": 20,
"scores": [
0.3930389999... | [
{
"source_db": "ClinVar",
"source_id": "DDX51",
"text": "NC_000012.11:g.(?_132414268)_(133263901_?)del VARIANT_IN_GENE DDX51",
"confidence": 1
}
] | {
"variant": "NC_000012.11:g.(?_132414268)_(133263901_?)del",
"gene": "DDX51",
"mean_phylop": -0.533,
"track": "phyloP100way"
} | 1 |
co_cons_00068 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000007.13:g.(?_55086755)_(55274084_?)del (in gene EGFR), classify the evolutionary constraint across the variant's genomic window. | NC_000007.13:g.(?_55086755)_(55274084_?)del VARIANT_IN_GENE EGFR | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000007.13:g.(?_55086755)_(55274084_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000007.13:g.(?_55086755)_(55274084_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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": "NC_000007.13:g.(?_55086755)_(55274084_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 55086755,
"track": "phyloP100way",
"window": 20,
"scores": [
1.03743,
... | [
{
"source_db": "ClinVar",
"source_id": "EGFR",
"text": "NC_000007.13:g.(?_55086755)_(55274084_?)del VARIANT_IN_GENE EGFR",
"confidence": 1
}
] | {
"variant": "NC_000007.13:g.(?_55086755)_(55274084_?)del",
"gene": "EGFR",
"mean_phylop": 0.366,
"track": "phyloP100way"
} | 1 |
co_cons_00069 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000003.11:g.(?_16710965)_(41275270_?)del (in gene MOBP), classify the evolutionary constraint across the variant's genomic window. | NC_000003.11:g.(?_16710965)_(41275270_?)del VARIANT_IN_GENE MOBP | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000003.11:g.(?_16710965)_(41275270_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000003.11:g.(?_16710965)_(41275270_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | 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": "NC_000003.11:g.(?_16710965)_(41275270_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 16710965,
"track": "phyloP100way",
"window": 20,
"scores": [
0.319,
0... | [
{
"source_db": "ClinVar",
"source_id": "MOBP",
"text": "NC_000003.11:g.(?_16710965)_(41275270_?)del VARIANT_IN_GENE MOBP",
"confidence": 1
}
] | {
"variant": "NC_000003.11:g.(?_16710965)_(41275270_?)del",
"gene": "MOBP",
"mean_phylop": 0.152,
"track": "phyloP100way"
} | 1 |
co_cons_00070 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 2q32.2-34(chr2:189909904-209468383)x1 (in gene ABI2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 2q32.2-34(chr2:189909904-209468383)x1 VARIANT_IN_GENE ABI2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 2q32.2-34(chr2:189909904-209468383)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 2q32.2-34(chr2:189909904-209468383)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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 2q32.2-34(chr2:189909904-209468383)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 189909904,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.146748... | [
{
"source_db": "ClinVar",
"source_id": "ABI2",
"text": "GRCh37/hg19 2q32.2-34(chr2:189909904-209468383)x1 VARIANT_IN_GENE ABI2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 2q32.2-34(chr2:189909904-209468383)x1",
"gene": "ABI2",
"mean_phylop": 0.064,
"track": "phyloP100way"
} | 1 |
co_cons_00071 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000455.5(STK11):c.785dup (p.Leu263fs) (in gene STK11), classify the evolutionary constraint across the variant's genomic window. | NM_000455.5(STK11):c.785dup (p.Leu263fs) VARIANT_IN_GENE STK11 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000455.5(STK11):c.785dup (p.Leu263fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000455.5(STK11):c.785dup (p.Leu263fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | 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_000455.5(STK11):c.785dup (p.Leu263fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr19",
"pos": 1221261,
"track": "phyloP100way",
"window": 20,
"scores": [
6.11771,
7.... | [
{
"source_db": "ClinVar",
"source_id": "STK11",
"text": "NM_000455.5(STK11):c.785dup (p.Leu263fs) VARIANT_IN_GENE STK11",
"confidence": 1
}
] | {
"variant": "NM_000455.5(STK11):c.785dup (p.Leu263fs)",
"gene": "STK11",
"mean_phylop": 6.13,
"track": "phyloP100way"
} | 1 |
co_cons_00072 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 12q24.32-24.33(chr12:126403612-133166920)x3 (in gene ADGRD1), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 12q24.32-24.33(chr12:126403612-133166920)x3 VARIANT_IN_GENE ADGRD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 12q24.32-24.33(chr12:126403612-133166920)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 12q24.32-24.33(chr12:126403612-133166920)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curate... | 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 12q24.32-24.33(chr12:126403612-133166920)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 126403612,
"track": "phyloP100way",
"window": 20,
"scores": [
-0... | [
{
"source_db": "ClinVar",
"source_id": "ADGRD1",
"text": "GRCh38/hg38 12q24.32-24.33(chr12:126403612-133166920)x3 VARIANT_IN_GENE ADGRD1",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 12q24.32-24.33(chr12:126403612-133166920)x3",
"gene": "ADGRD1",
"mean_phylop": 0.109,
"track": "phyloP100way"
} | 1 |
co_cons_00073 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1 (in gene AGAP2), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1 VARIANT_IN_GENE AGAP2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1",
"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 12q13.3-14.2(chr12:57013355-63042498)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 57013355,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.0709... | [
{
"source_db": "ClinVar",
"source_id": "AGAP2",
"text": "GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1 VARIANT_IN_GENE AGAP2",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 12q13.3-14.2(chr12:57013355-63042498)x1",
"gene": "AGAP2",
"mean_phylop": 0.919,
"track": "phyloP100way"
} | 1 |
co_cons_00074 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3 (in gene CCDC116), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3 VARIANT_IN_GENE CCDC116 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3",
"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"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 21798907,
"track": "phyloP100way",
"window": 20,
"scores": [
1.487... | [
{
"source_db": "ClinVar",
"source_id": "CCDC116",
"text": "GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3 VARIANT_IN_GENE CCDC116",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 22q11.21-11.22(chr22:21798907-22962962)x3",
"gene": "CCDC116",
"mean_phylop": -0.138,
"track": "phyloP100way"
} | 1 |
co_cons_00075 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 2q35-36.3(chr2:217374144-227643620)x1 (in gene ARPC2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 2q35-36.3(chr2:217374144-227643620)x1 VARIANT_IN_GENE ARPC2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 2q35-36.3(chr2:217374144-227643620)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 2q35-36.3(chr2:217374144-227643620)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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 2q35-36.3(chr2:217374144-227643620)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 217374144,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.687512... | [
{
"source_db": "ClinVar",
"source_id": "ARPC2",
"text": "GRCh37/hg19 2q35-36.3(chr2:217374144-227643620)x1 VARIANT_IN_GENE ARPC2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 2q35-36.3(chr2:217374144-227643620)x1",
"gene": "ARPC2",
"mean_phylop": 0.057,
"track": "phyloP100way"
} | 1 |
co_cons_00076 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1 (in gene DPY19L1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1 VARIANT_IN_GENE DPY19L1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | 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": "GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 33478398,
"track": "phyloP100way",
"window": 20,
"scores": [
0.280827,
... | [
{
"source_db": "ClinVar",
"source_id": "DPY19L1",
"text": "GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1 VARIANT_IN_GENE DPY19L1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1",
"gene": "DPY19L1",
"mean_phylop": 0.459,
"track": "phyloP100way"
} | 1 |
co_cons_00077 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_012179.4(FBXO7):c.1408G>T (p.Glu470Ter) (in gene FBXO7), classify the evolutionary constraint across the variant's genomic window. | NM_012179.4(FBXO7):c.1408G>T (p.Glu470Ter) VARIANT_IN_GENE FBXO7 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_012179.4(FBXO7):c.1408G>T (p.Glu470Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_012179.4(FBXO7):c.1408G>T (p.Glu470Ter)",
"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_012179.4(FBXO7):c.1408G>T (p.Glu470Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 32498369,
"track": "phyloP100way",
"window": 20,
"scores": [
5.40002,
... | [
{
"source_db": "ClinVar",
"source_id": "FBXO7",
"text": "NM_012179.4(FBXO7):c.1408G>T (p.Glu470Ter) VARIANT_IN_GENE FBXO7",
"confidence": 1
}
] | {
"variant": "NM_012179.4(FBXO7):c.1408G>T (p.Glu470Ter)",
"gene": "FBXO7",
"mean_phylop": 2.034,
"track": "phyloP100way"
} | 1 |
co_cons_00078 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_138576.4(BCL11B):c.1916_1917dup (p.Gly640fs) (in gene BCL11B), classify the evolutionary constraint across the variant's genomic window. | NM_138576.4(BCL11B):c.1916_1917dup (p.Gly640fs) VARIANT_IN_GENE BCL11B | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_138576.4(BCL11B):c.1916_1917dup (p.Gly640fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_138576.4(BCL11B):c.1916_1917dup (p.Gly640fs)",
"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_138576.4(BCL11B):c.1916_1917dup (p.Gly640fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 99174918,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.24791,
... | [
{
"source_db": "ClinVar",
"source_id": "BCL11B",
"text": "NM_138576.4(BCL11B):c.1916_1917dup (p.Gly640fs) VARIANT_IN_GENE BCL11B",
"confidence": 1
}
] | {
"variant": "NM_138576.4(BCL11B):c.1916_1917dup (p.Gly640fs)",
"gene": "BCL11B",
"mean_phylop": 2.086,
"track": "phyloP100way"
} | 1 |
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