id stringlengths 13 13 | task_type stringclasses 6
values | pipeline stringclasses 1
value | difficulty stringclasses 3
values | num_hops int64 1 5 | question stringlengths 94 258 | context stringlengths 41 511 | reasoning_chain dict | answer stringlengths 1 511 | modalities listlengths 1 3 | modality_data listlengths 1 5 | evidence listlengths 1 5 | metadata stringlengths 49 912 | path_confidence_score float64 0.61 1 | choices listlengths 4 4 ⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
no_dise_00435 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FGFR1 classified as Pathogenic or Likely Pathogenic for Hypogonadotropic hypogonadism. | NM_023110.3(FGFR1):c.670G>C (p.Asp224His) VARIANT_IN_GENE FGFR1 → NM_023110.3(FGFR1):c.670G>C (p.Asp224His) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hypogonadotropic hypogonadism | {
"steps": [
{
"hop": 1,
"source_node_id": "FGFR1",
"source_node_type": "GENE",
"source_node_label": "FGFR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_023110.3... | NM_023110.3(FGFR1):c.670G>C (p.Asp224His) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FGFR1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FGFR1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_023110.3(FGFR1):c.670G>C (p.Asp224His)",
"text": "NM_023110.3(FGFR1):c.670G>C (p.Asp224His) VARIANT_IN_GENE FGFR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hypogonadotropic_hypogonadism",
"text": "NM_023110.3(FGFR1... | {"gene": "FGFR1", "disease": "Hypogonadotropic hypogonadism", "pathogenic_variants": ["NM_023110.3(FGFR1):c.729C>A (p.Tyr243Ter)", "NM_023110.3(FGFR1):c.1716C>G (p.Tyr572Ter)", "NM_023110.3(FGFR1):c.1029G>A (p.Ala343=)", "NM_023110.3(FGFR1):c.670G>C (p.Asp224His)"]} | 0.921954 | null |
no_dise_00294 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for BRAF-related disorder. | NM_004333.6(BRAF):c.722C>T (p.Thr241Met) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.722C>T (p.Thr241Met) VARIANT_HAS_CLINICAL_SIGNIFICANCE BRAF-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.722C>T (p.Thr241Met) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.722C>T (p.Thr241Met)",
"text": "NM_004333.6(BRAF):c.722C>T (p.Thr241Met) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:braf_related_disorder",
"text": "NM_004333.6(BRAF):c.722C>T (... | {"gene": "BRAF", "disease": "BRAF-related disorder", "pathogenic_variants": ["NM_004333.6(BRAF):c.1502A>C (p.Glu501Ala)", "NM_004333.6(BRAF):c.1403T>C (p.Phe468Ser)", "NM_004333.6(BRAF):c.722C>T (p.Thr241Met)"]} | 0.921954 | null |
no_dise_00185 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FAT4 classified as Pathogenic or Likely Pathogenic for Autosomal recessive FAT4-related disorders. | NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) VARIANT_IN_GENE FAT4 → NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Autosomal recessive FAT4-related disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "FAT4",
"source_node_type": "GENE",
"source_node_label": "FAT4",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001291303.... | NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FAT4\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FAT4\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter)",
"text": "NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) VARIANT_IN_GENE FAT4",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:autosomal_recessive_fat4_related_disorders",
"text"... | {"gene": "FAT4", "disease": "Autosomal recessive FAT4-related disorders", "pathogenic_variants": ["NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter)"]} | 0.921954 | null |
no_dise_00345 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FGFR1 classified as Pathogenic or Likely Pathogenic for Autosomal recessive FGFR1-related disorders. | NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) VARIANT_IN_GENE FGFR1 → NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Autosomal recessive FGFR1-related disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "FGFR1",
"source_node_type": "GENE",
"source_node_label": "FGFR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_023110.3... | NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FGFR1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FGFR1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg)",
"text": "NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) VARIANT_IN_GENE FGFR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:autosomal_recessive_fgfr1_related_disorders",
"text": "N... | {"gene": "FGFR1", "disease": "Autosomal recessive FGFR1-related disorders", "pathogenic_variants": ["NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg)"]} | 0.83666 | null |
no_dise_00571 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NOTCH1 classified as Pathogenic or Likely Pathogenic for Adams-Oliver syndrome 5. | NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) VARIANT_IN_GENE NOTCH1 → NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE Adams-Oliver syndrome 5 | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_017617... | NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NOTCH1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NOTCH1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer)",
"text": "NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:adams_oliver_synd... | {"gene": "NOTCH1", "disease": "Adams-Oliver syndrome 5", "pathogenic_variants": ["Single allele", "NM_017617.5(NOTCH1):c.1342del (p.Arg448fs)", "NM_017617.5(NOTCH1):c.1650C>A (p.Tyr550Ter)", "NM_017617.5(NOTCH1):c.3963del (p.Cys1322fs)", "NM_017617.5(NOTCH1):c.5164C>T (p.Gln1722Ter)", "NM_017617.5(NOTCH1):c.2157_2158in... | 0.83666 | null |
no_dise_00192 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA2 classified as Pathogenic or Likely Pathogenic for Breast-ovarian cancer, familial, susceptibility to, 2. | NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) VARIANT_IN_GENE BRCA2 → NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast-ovarian cancer, familial, susceptibility to, 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000059.4... | NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer)",
"text": "NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_ovarian_cancer_familial_susce... | {"gene": "BRCA2", "disease": "Breast-ovarian cancer, familial, susceptibility to, 2", "pathogenic_variants": ["NM_000059.4(BRCA2):c.6577G>T (p.Glu2193Ter)", "NM_000059.4(BRCA2):c.4658del (p.Thr1553fs)", "NM_000059.4(BRCA2):c.6065C>A (p.Ser2022Ter)", "NM_000059.4(BRCA2):c.8108_8115delinsTATATAAATAAATAAATAAATATATATTTATTT... | 0.83666 | null |
no_dise_00115 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CHEK2 classified as Pathogenic or Likely Pathogenic for CHEK2-related cancer predisposition. | NM_007194.4(CHEK2):c.1461+1del VARIANT_IN_GENE CHEK2 → NM_007194.4(CHEK2):c.1461+1del VARIANT_HAS_CLINICAL_SIGNIFICANCE CHEK2-related cancer predisposition | {
"steps": [
{
"hop": 1,
"source_node_id": "CHEK2",
"source_node_type": "GENE",
"source_node_label": "CHEK2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007194.4... | NM_007194.4(CHEK2):c.1461+1del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CHEK2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CHEK2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_007194.4(CHEK2):c.1461+1del",
"text": "NM_007194.4(CHEK2):c.1461+1del VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:chek2_related_cancer_predisposition",
"text": "NM_007194.4(CHEK2):c.1461+1del VA... | {"gene": "CHEK2", "disease": "CHEK2-related cancer predisposition", "pathogenic_variants": ["NM_007194.4:c.(908+21_909-21)_(1095+21_1096-21)del", "NC_000022.11:g.(?_29092888)_(29095925_?)del", "NC_000022.11:g.(?_29120964)_(29121355_?)del", "NC_000022.11:g.(?_29105993)_(29108005_?)del", "NM_007194.4(CHEK2):c.1241del (p.... | 0.921954 | null |
no_dise_00374 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DNMT3A classified as Pathogenic or Likely Pathogenic for EBV-positive nodal T- and NK-cell lymphoma. | NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) VARIANT_IN_GENE DNMT3A → NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE EBV-positive nodal T- and NK-cell lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_022552... | NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DNMT3A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DNMT3A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter)",
"text": "NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) VARIANT_IN_GENE DNMT3A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:ebv_positive_nodal_t_and_nk_cell_lymphoma",
"text": "... | {"gene": "DNMT3A", "disease": "EBV-positive nodal T- and NK-cell lymphoma", "pathogenic_variants": ["NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter)", "NM_022552.5(DNMT3A):c.2250del (p.Phe751fs)", "NM_022552.5(DNMT3A):c.754_760dup (p.Ala254fs)"]} | 0.707107 | null |
no_dise_00163 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in AFP classified as Pathogenic or Likely Pathogenic for Alpha-fetoprotein deficiency. | NM_001134.3(AFP):c.883_884del (p.Leu295fs) VARIANT_IN_GENE AFP → NM_001134.3(AFP):c.883_884del (p.Leu295fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Alpha-fetoprotein deficiency | {
"steps": [
{
"hop": 1,
"source_node_id": "AFP",
"source_node_type": "GENE",
"source_node_label": "AFP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001134.3(AFP... | NM_001134.3(AFP):c.883_884del (p.Leu295fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"AFP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"AFP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_001134.3(AFP):c.883_884del (p.Leu295fs)",
"text": "NM_001134.3(AFP):c.883_884del (p.Leu295fs) VARIANT_IN_GENE AFP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:alpha_fetoprotein_deficiency",
"text": "NM_001134.3(AFP):c... | {"gene": "AFP", "disease": "Alpha-fetoprotein deficiency", "pathogenic_variants": ["NM_001134.3(AFP):c.543G>A (p.Trp181Ter)", "NM_001134.3(AFP):c.883_884del (p.Leu295fs)"]} | 0.707107 | null |
no_dise_00410 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DCTN1 classified as Pathogenic or Likely Pathogenic for DCTN1-related disorder. | NM_004082.5(DCTN1):c.279+1G>T VARIANT_IN_GENE DCTN1 → NM_004082.5(DCTN1):c.279+1G>T VARIANT_HAS_CLINICAL_SIGNIFICANCE DCTN1-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "DCTN1",
"source_node_type": "GENE",
"source_node_label": "DCTN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004082.5... | NM_004082.5(DCTN1):c.279+1G>T | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DCTN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DCTN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_004082.5(DCTN1):c.279+1G>T",
"text": "NM_004082.5(DCTN1):c.279+1G>T VARIANT_IN_GENE DCTN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:dctn1_related_disorder",
"text": "NM_004082.5(DCTN1):c.279+1G>T VARIANT_HAS_CLINIC... | {"gene": "DCTN1", "disease": "DCTN1-related disorder", "pathogenic_variants": ["NM_004082.5(DCTN1):c.279+1G>T"]} | 0.921954 | null |
no_dise_00070 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in VPS35 classified as Pathogenic or Likely Pathogenic for Parkinson disease 17. | NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) VARIANT_IN_GENE VPS35 → NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE Parkinson disease 17 | {
"steps": [
{
"hop": 1,
"source_node_id": "VPS35",
"source_node_type": "GENE",
"source_node_label": "VPS35",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_018206.6... | NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"VPS35\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"VPS35\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu)",
"text": "NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) VARIANT_IN_GENE VPS35",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:parkinson_disease_17",
"text": "NM_018206.6(VPS35):c.214... | {"gene": "VPS35", "disease": "Parkinson disease 17", "pathogenic_variants": ["NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu)"]} | 0.83666 | null |
no_dise_00494 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA1 classified as Pathogenic or Likely Pathogenic for Inherited ovarian cancer (without breast cancer). | NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) VARIANT_IN_GENE BRCA1 → NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited ovarian cancer (without breast cancer) | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007294.4... | NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg)",
"text": "NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_ovarian_cancer_without_breast_cancer",
"text... | {"gene": "BRCA1", "disease": "Inherited ovarian cancer (without breast cancer)", "pathogenic_variants": ["NM_007294.4(BRCA1):c.2850_2851del (p.Arg951fs)", "NM_007294.4(BRCA1):c.135-1G>A", "NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg)"]} | 0.921954 | null |
no_dise_00412 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in ABL1 classified as Pathogenic or Likely Pathogenic for Leukemia, Philadelphia chromosome-positive, resistant to imatinib. | NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) VARIANT_IN_GENE ABL1 → NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Leukemia, Philadelphia chromosome-positive, resistant to imatinib | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005157.6(A... | NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"ABL1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"ABL1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_005157.6(ABL1):c.706G>A (p.Glu236Lys)",
"text": "NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) VARIANT_IN_GENE ABL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:leukemia_philadelphia_chromosome_positive_resistant_to_imati",
... | {"gene": "ABL1", "disease": "Leukemia, Philadelphia chromosome-positive, resistant to imatinib", "pathogenic_variants": ["NM_005157.6(ABL1):c.757T>C (p.Tyr253His)", "NM_005157.6(ABL1):c.706G>A (p.Glu236Lys)", "NM_005157.6(ABL1):c.707A>T (p.Glu236Val)"]} | 0.707107 | null |
no_dise_00157 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PDE10A classified as Pathogenic or Likely Pathogenic for Infantile-onset generalized dyskinesia with orofacial involvement. | NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) VARIANT_IN_GENE PDE10A → NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Infantile-onset generalized dyskinesia with orofacial involvement | {
"steps": [
{
"hop": 1,
"source_node_id": "PDE10A",
"source_node_type": "GENE",
"source_node_label": "PDE10A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001385... | NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PDE10A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PDE10A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys)",
"text": "NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) VARIANT_IN_GENE PDE10A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:infantile_onset_generalized_dyskinesia_with_orofaci... | {"gene": "PDE10A", "disease": "Infantile-onset generalized dyskinesia with orofacial involvement", "pathogenic_variants": ["NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys)", "NM_001385079.1(PDE10A):c.1144G>C (p.Ala382Pro)", "NM_001385079.1(PDE10A):c.686del (p.Gly229fs)", "NM_001385079.1(PDE10A):c.193_200dup (p.Pro68fs)"... | 0.921954 | null |
no_dise_00198 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DNMT3A classified as Pathogenic or Likely Pathogenic for Hydrocephalus, nonsyndromic, autosomal recessive 2. | GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 VARIANT_IN_GENE DNMT3A → GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 VARIANT_HAS_CLINICAL_SIGNIFICANCE Hydrocephalus, nonsyndromic, autosomal recessive 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "GRCh37/hg... | GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DNMT3A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DNMT3A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1",
"text": "GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 VARIANT_IN_GENE DNMT3A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hydrocephalus_nonsyndromic_autosomal_recessive_2",
... | {"gene": "DNMT3A", "disease": "Hydrocephalus, nonsyndromic, autosomal recessive 2", "pathogenic_variants": ["GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1"]} | 0.83666 | null |
no_dise_00601 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA2 classified as Pathogenic or Likely Pathogenic for Breast-ovarian cancer, familial, susceptibility to, 1. | NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) VARIANT_IN_GENE BRCA2 → NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast-ovarian cancer, familial, susceptibility to, 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000059.4... | NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs)",
"text": "NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_ovarian_cancer_familial_susceptibility_to_1",... | {"gene": "BRCA2", "disease": "Breast-ovarian cancer, familial, susceptibility to, 1", "pathogenic_variants": ["NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs)", "NM_000059.4(BRCA2):c.1094del (p.Pro365fs)", "NM_000059.4(BRCA2):c.4361_4368delinsTCAGAT (p.Pro1454fs)"]} | 0.83666 | null |
no_dise_00018 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KMT2C classified as Pathogenic or Likely Pathogenic for KMT2C-related disorder. | NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) VARIANT_IN_GENE KMT2C → NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) VARIANT_HAS_CLINICAL_SIGNIFICANCE KMT2C-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_170606.3... | NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KMT2C\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KMT2C\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser)",
"text": "NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:kmt2c_related_disorder",
"text": "NM_170606.3(KMT2C)... | {"gene": "KMT2C", "disease": "KMT2C-related disorder", "pathogenic_variants": ["NM_170606.3(KMT2C):c.8026C>T (p.Gln2676Ter)", "NM_170606.3(KMT2C):c.10449dup (p.Gln3484fs)", "NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser)", "NM_170606.3(KMT2C):c.4272del (p.His1424fs)"]} | 0.83666 | null |
no_dise_00384 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for Paediatric disorders. | NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) VARIANT_HAS_CLINICAL_SIGNIFICANCE Paediatric disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile)",
"text": "NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:paediatric_disorders",
"text": "NM_004333.6(BRAF):c.1729C>A... | {"gene": "BRAF", "disease": "Paediatric disorders", "pathogenic_variants": ["NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile)"]} | 0.83666 | null |
no_dise_00278 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MSH2 classified as Pathogenic or Likely Pathogenic for Uterine corpus cancer. | NM_000251.2(MSH2):c.2459-2_2472del VARIANT_IN_GENE MSH2 → NM_000251.2(MSH2):c.2459-2_2472del VARIANT_HAS_CLINICAL_SIGNIFICANCE Uterine corpus cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000251.2(M... | NM_000251.2(MSH2):c.2459-2_2472del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MSH2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MSH2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000251.2(MSH2):c.2459-2_2472del",
"text": "NM_000251.2(MSH2):c.2459-2_2472del VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:uterine_corpus_cancer",
"text": "NM_000251.2(MSH2):c.2459-2_2472del VARIA... | {"gene": "MSH2", "disease": "Uterine corpus cancer", "pathogenic_variants": ["NM_000251.2(MSH2):c.2459-2_2472del"]} | 0.707107 | null |
no_dise_00277 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA2 classified as Pathogenic or Likely Pathogenic for BRCA2-related cancer predisposition. | NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) VARIANT_IN_GENE BRCA2 → NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE BRCA2-related cancer predisposition | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000059.4... | NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.6052del (p.Ser2018fs)",
"text": "NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:brca2_related_cancer_predisposition",
"text": "NM_000059... | {"gene": "BRCA2", "disease": "BRCA2-related cancer predisposition", "pathogenic_variants": ["NM_000059.4:c.(1_67+1)del", "NM_000059.4(BRCA2):c.5112_5119delinsG (p.Ile1705fs)", "NM_000059.4(BRCA2):c.8754+1152_9256del", "NM_000059.4(BRCA2):c.8633-6_8635del", "NM_000059.4(BRCA2):c.8469_8478delinsTA (p.Gln2823fs)", "NM_000... | 0.921954 | null |
no_dise_00180 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CHEK2 classified as Pathogenic or Likely Pathogenic for Congenital heart defects, multiple types, 3. | NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) VARIANT_IN_GENE CHEK2 → NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Congenital heart defects, multiple types, 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "CHEK2",
"source_node_type": "GENE",
"source_node_label": "CHEK2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007194.4... | NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CHEK2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CHEK2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter)",
"text": "NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:congenital_heart_defects_multiple_types_3",
"text": "NM_00... | {"gene": "CHEK2", "disease": "Congenital heart defects, multiple types, 3", "pathogenic_variants": ["NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter)"]} | 0.921954 | null |
no_dise_00122 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CBL classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases. | NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) VARIANT_IN_GENE CBL → NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "CBL",
"source_node_type": "GENE",
"source_node_label": "CBL",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005188.4(CBL... | NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CBL\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CBL\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_005188.4(CBL):c.1166A>C (p.Lys389Thr)",
"text": "NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) VARIANT_IN_GENE CBL",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_005188.4(CBL):c.1166A>C ... | {"gene": "CBL", "disease": "Inborn genetic diseases", "pathogenic_variants": ["NM_005188.4(CBL):c.1166A>C (p.Lys389Thr)"]} | 0.921954 | null |
no_dise_00593 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RET classified as Pathogenic or Likely Pathogenic for Medullary thyroid carcinoma. | NM_020975.6(RET):c.2671T>G (p.Ser891Ala) VARIANT_IN_GENE RET → NM_020975.6(RET):c.2671T>G (p.Ser891Ala) VARIANT_HAS_CLINICAL_SIGNIFICANCE Medullary thyroid carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_020975.6(RET... | NM_020975.6(RET):c.2671T>G (p.Ser891Ala) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RET\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RET\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_020975.6(RET):c.2671T>G (p.Ser891Ala)",
"text": "NM_020975.6(RET):c.2671T>G (p.Ser891Ala) VARIANT_IN_GENE RET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:medullary_thyroid_carcinoma",
"text": "NM_020975.6(RET):c.2671... | {"gene": "RET", "disease": "Medullary thyroid carcinoma", "pathogenic_variants": ["NM_020975.6(RET):c.2671T>G (p.Ser891Ala)"]} | 0.921954 | null |
no_dise_00428 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in ANXA11 classified as Pathogenic or Likely Pathogenic for Amyotrophic lateral sclerosis type 23. | NM_145868.2(ANXA11):c.744+1G>A VARIANT_IN_GENE ANXA11 → NM_145868.2(ANXA11):c.744+1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE Amyotrophic lateral sclerosis type 23 | {
"steps": [
{
"hop": 1,
"source_node_id": "ANXA11",
"source_node_type": "GENE",
"source_node_label": "ANXA11",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_145868... | NM_145868.2(ANXA11):c.744+1G>A | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"ANXA11\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"ANXA11\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_145868.2(ANXA11):c.744+1G>A",
"text": "NM_145868.2(ANXA11):c.744+1G>A VARIANT_IN_GENE ANXA11",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:amyotrophic_lateral_sclerosis_type_23",
"text": "NM_145868.2(ANXA11):c.744+1G>A... | {"gene": "ANXA11", "disease": "Amyotrophic lateral sclerosis type 23", "pathogenic_variants": ["NM_145868.2(ANXA11):c.744+1G>A", "NM_145868.2(ANXA11):c.118G>T (p.Asp40Tyr)", "NM_145868.2(ANXA11):c.112G>A (p.Gly38Arg)", "NM_145868.2(ANXA11):c.119A>G (p.Asp40Gly)"]} | 0.83666 | null |
no_dise_00580 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CREBBP classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases. | NM_004380.3(CREBBP):c.90del (p.Phe30fs) VARIANT_IN_GENE CREBBP → NM_004380.3(CREBBP):c.90del (p.Phe30fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004380... | NM_004380.3(CREBBP):c.90del (p.Phe30fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CREBBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CREBBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_004380.3(CREBBP):c.90del (p.Phe30fs)",
"text": "NM_004380.3(CREBBP):c.90del (p.Phe30fs) VARIANT_IN_GENE CREBBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_004380.3(CREBBP):c.90de... | {"gene": "CREBBP", "disease": "Inborn genetic diseases", "pathogenic_variants": ["NM_004380.3(CREBBP):c.3G>T (p.Met1Ile)", "NM_004380.3(CREBBP):c.1948T>C (p.Tyr650His)", "NM_004380.3(CREBBP):c.6271A>T (p.Lys2091Ter)", "NM_004380.3(CREBBP):c.4495C>G (p.Leu1499Val)", "NM_004380.3(CREBBP):c.3625C>T (p.Gln1209Ter)", "NM_00... | 0.83666 | null |
no_dise_00594 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NF1 classified as Pathogenic or Likely Pathogenic for Developmental defect during embryogenesis. | NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) VARIANT_IN_GENE NF1 → NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE Developmental defect during embryogenesis | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001042492.3(... | NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NF1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NF1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer)",
"text": "NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) VARIANT_IN_GENE NF1",
"confidence": 1
},
{
"source_... | {"gene": "NF1", "disease": "Developmental defect during embryogenesis", "pathogenic_variants": ["NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer)"]} | 0.83666 | null |
no_dise_00222 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in TARDBP classified as Pathogenic or Likely Pathogenic for Frontotemporal dementia. | NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) VARIANT_IN_GENE TARDBP → NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) VARIANT_HAS_CLINICAL_SIGNIFICANCE Frontotemporal dementia | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007375... | NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"TARDBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"TARDBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro)",
"text": "NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) VARIANT_IN_GENE TARDBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:frontotemporal_dementia",
"text": "NM_007375.4(TARDBP... | {"gene": "TARDBP", "disease": "Frontotemporal dementia", "pathogenic_variants": ["NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro)"]} | 0.83666 | null |
no_dise_00463 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRIP1 classified as Pathogenic or Likely Pathogenic for Inherited ovarian cancer (without breast cancer). | NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) VARIANT_IN_GENE BRIP1 → NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited ovarian cancer (without breast cancer) | {
"steps": [
{
"hop": 1,
"source_node_id": "BRIP1",
"source_node_type": "GENE",
"source_node_label": "BRIP1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_032043.3... | NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRIP1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRIP1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter)",
"text": "NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) VARIANT_IN_GENE BRIP1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_ovarian_cancer_without_breast_cancer",
"text":... | {"gene": "BRIP1", "disease": "Inherited ovarian cancer (without breast cancer)", "pathogenic_variants": ["NM_032043.3(BRIP1):c.688del (p.Ser230fs)", "NM_032043.3(BRIP1):c.1888dup (p.Thr630fs)", "NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter)", "NM_032043.3(BRIP1):c.1495C>T (p.Gln499Ter)", "NM_032043.3(BRIP1):c.918+1G>A", "... | 0.921954 | null |
no_dise_00394 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KDM6A classified as Pathogenic or Likely Pathogenic for Kabuki syndrome 1. | NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) VARIANT_IN_GENE KDM6A → NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Kabuki syndrome 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "KDM6A",
"source_node_type": "GENE",
"source_node_label": "KDM6A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_00129141... | NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KDM6A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KDM6A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_001291415.2(KDM6A):c.133dup (p.Glu45fs)",
"text": "NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) VARIANT_IN_GENE KDM6A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:kabuki_syndrome_1",
"text": "NM_001291415.2(KDM6A):c.133... | {"gene": "KDM6A", "disease": "Kabuki syndrome 1", "pathogenic_variants": ["NM_001291415.2(KDM6A):c.133dup (p.Glu45fs)"]} | 0.83666 | null |
no_dise_00488 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BCHE classified as Pathogenic or Likely Pathogenic for BCHE Newfoundland. | BCHE Newfoundland VARIANT_IN_GENE BCHE → BCHE Newfoundland VARIANT_HAS_CLINICAL_SIGNIFICANCE BCHE Newfoundland | {
"steps": [
{
"hop": 1,
"source_node_id": "BCHE",
"source_node_type": "GENE",
"source_node_label": "BCHE",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "BCHE Newfound... | BCHE Newfoundland | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BCHE\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BCHE\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "BCHE Newfoundland",
"text": "BCHE Newfoundland VARIANT_IN_GENE BCHE",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:bche_newfoundland",
"text": "BCHE Newfoundland VARIANT_HAS_CLINICAL_SIGNIFICANCE BCHE Newfoundland",
"c... | {"gene": "BCHE", "disease": "BCHE Newfoundland", "pathogenic_variants": ["BCHE Newfoundland"]} | 0.707107 | null |
no_dise_00466 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in TARDBP classified as Pathogenic or Likely Pathogenic for FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED. | NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_IN_GENE TARDBP → NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007375... | NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"TARDBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"TARDBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu)",
"text": "NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_IN_GENE TARDBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:frontotemporal_dementia_with_tdp43_inclusions_tardbp_relate... | {"gene": "TARDBP", "disease": "FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED", "pathogenic_variants": ["NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu)"]} | 0.707107 | null |
no_dise_00584 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for LEOPARD syndrome 3. | NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) VARIANT_HAS_CLINICAL_SIGNIFICANCE LEOPARD syndrome 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln)",
"text": "NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:leopard_syndrome_3",
"text": "NM_004333.6(BRAF):c.1801A>C (... | {"gene": "BRAF", "disease": "LEOPARD syndrome 3", "pathogenic_variants": ["NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln)", "NM_004333.6(BRAF):c.1802A>T (p.Lys601Ile)"]} | 0.921954 | null |
no_dise_00592 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CDH1 classified as Pathogenic or Likely Pathogenic for Malignant tumor of breast. | NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del VARIANT_IN_GENE CDH1 → NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del VARIANT_HAS_CLINICAL_SIGNIFICANCE Malignant tumor of breast | {
"steps": [
{
"hop": 1,
"source_node_id": "CDH1",
"source_node_type": "GENE",
"source_node_label": "CDH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000016.9:g... | NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CDH1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CDH1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del",
"text": "NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del VARIANT_IN_GENE CDH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:malignant_tumor_of_breast",
"... | {"gene": "CDH1", "disease": "Malignant tumor of breast", "pathogenic_variants": ["NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del", "NM_004360.5(CDH1):c.2440-2_*1del", "NC_000016.9:g.(68857530_68862076)_(68863701_68867192)dup"]} | 0.83666 | null |
no_dise_00485 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CTNNA1 classified as Pathogenic or Likely Pathogenic for Craniosynostosis syndrome. | NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) VARIANT_IN_GENE CTNNA1 → NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) VARIANT_HAS_CLINICAL_SIGNIFICANCE Craniosynostosis syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNA1",
"source_node_type": "GENE",
"source_node_label": "CTNNA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001903... | NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CTNNA1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CTNNA1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup)",
"text": "NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) VARIANT_IN_GENE CTNNA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:craniosynostosis_syndrome",
"... | {"gene": "CTNNA1", "disease": "Craniosynostosis syndrome", "pathogenic_variants": ["NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup)"]} | 0.707107 | null |
no_dise_00272 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RAD51D classified as Pathogenic or Likely Pathogenic for Familial ovarian cancer. | NM_002878.4(RAD51D):c.536dup (p.Asp180fs) VARIANT_IN_GENE RAD51D → NM_002878.4(RAD51D):c.536dup (p.Asp180fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Familial ovarian cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51D",
"source_node_type": "GENE",
"source_node_label": "RAD51D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002878... | NM_002878.4(RAD51D):c.536dup (p.Asp180fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RAD51D\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RAD51D\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.536dup (p.Asp180fs)",
"text": "NM_002878.4(RAD51D):c.536dup (p.Asp180fs) VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:familial_ovarian_cancer",
"text": "NM_002878.4(RAD51D):c.... | {"gene": "RAD51D", "disease": "Familial ovarian cancer", "pathogenic_variants": ["NM_002878.4(RAD51D):c.547C>T (p.Gln183Ter)", "NM_002878.4(RAD51D):c.748del (p.His250fs)", "NM_002878.4(RAD51D):c.536dup (p.Asp180fs)", "NM_002878.4(RAD51D):c.144+1G>A"]} | 0.83666 | null |
no_dise_00006 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PMS2 classified as Pathogenic or Likely Pathogenic for PMS2-related disorder. | NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) VARIANT_IN_GENE PMS2 → NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE PMS2-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000535.7(P... | NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PMS2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PMS2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter)",
"text": "NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:pms2_related_disorder",
"text": "NM_000535.7(PMS2):c.1438G>... | {"gene": "PMS2", "disease": "PMS2-related disorder", "pathogenic_variants": ["NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter)"]} | 0.707107 | null |
no_dise_00343 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RET classified as Pathogenic or Likely Pathogenic for Abnormality of the digestive system. | NM_020975.6(RET):c.960del (p.Asp322fs) VARIANT_IN_GENE RET → NM_020975.6(RET):c.960del (p.Asp322fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Abnormality of the digestive system | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_020975.6(RET... | NM_020975.6(RET):c.960del (p.Asp322fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RET\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RET\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_020975.6(RET):c.960del (p.Asp322fs)",
"text": "NM_020975.6(RET):c.960del (p.Asp322fs) VARIANT_IN_GENE RET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:abnormality_of_the_digestive_system",
"text": "NM_020975.6(RET):c.... | {"gene": "RET", "disease": "Abnormality of the digestive system", "pathogenic_variants": ["NM_020975.6(RET):c.960del (p.Asp322fs)"]} | 0.83666 | null |
no_dise_00368 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RAD51D classified as Pathogenic or Likely Pathogenic for Deleterious RAD51D Gene Mutation. | NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) VARIANT_IN_GENE RAD51D → NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Deleterious RAD51D Gene Mutation | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51D",
"source_node_type": "GENE",
"source_node_label": "RAD51D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002878... | NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RAD51D\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RAD51D\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter)",
"text": "NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:deleterious_rad51d_gene_mutation",
"text": "NM_002878.4... | {"gene": "RAD51D", "disease": "Deleterious RAD51D Gene Mutation", "pathogenic_variants": ["NM_002878.4(RAD51D):c.564_567del (p.Val189fs)", "NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter)"]} | 0.83666 | null |
no_dise_00226 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PFN1 classified as Pathogenic or Likely Pathogenic for PAGET DISEASE OF BONE 7, EARLY-ONSET. | PFN1, 4-BP DEL, 318TGAC VARIANT_IN_GENE PFN1 → PFN1, 4-BP DEL, 318TGAC VARIANT_HAS_CLINICAL_SIGNIFICANCE PAGET DISEASE OF BONE 7, EARLY-ONSET | {
"steps": [
{
"hop": 1,
"source_node_id": "PFN1",
"source_node_type": "GENE",
"source_node_label": "PFN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "PFN1, 4-BP DE... | PFN1, 4-BP DEL, 318TGAC | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PFN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PFN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "PFN1, 4-BP DEL, 318TGAC",
"text": "PFN1, 4-BP DEL, 318TGAC VARIANT_IN_GENE PFN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:paget_disease_of_bone_7_early_onset",
"text": "PFN1, 4-BP DEL, 318TGAC VARIANT_HAS_CLINICAL_SIG... | {"gene": "PFN1", "disease": "PAGET DISEASE OF BONE 7, EARLY-ONSET", "pathogenic_variants": ["NM_005022.4(PFN1):c.325+10T>C", "PFN1, 1-BP DEL, 324G", "PFN1, 4-BP DEL, 318TGAC"]} | 0.707107 | null |
no_dise_00242 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in POLD1 classified as Pathogenic or Likely Pathogenic for Immunodeficiency 120. | NM_002691.4(POLD1):c.[2052G>C;2816C>G] VARIANT_IN_GENE POLD1 → NM_002691.4(POLD1):c.[2052G>C;2816C>G] VARIANT_HAS_CLINICAL_SIGNIFICANCE Immunodeficiency 120 | {
"steps": [
{
"hop": 1,
"source_node_id": "POLD1",
"source_node_type": "GENE",
"source_node_label": "POLD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002691.4... | NM_002691.4(POLD1):c.[2052G>C;2816C>G] | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"POLD1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"POLD1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_002691.4(POLD1):c.2052G>C (p.Gln684His)",
"text": "NM_002691.4(POLD1):c.[2052G>C;2816C>G] VARIANT_IN_GENE POLD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:immunodeficiency_120",
"text": "NM_002691.4(POLD1):c.[2052G>... | {"gene": "POLD1", "disease": "Immunodeficiency 120", "pathogenic_variants": ["NM_002691.4(POLD1):c.[2052G>C;2816C>G]"]} | 0.707107 | null |
no_dise_00610 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NLRP3 classified as Pathogenic or Likely Pathogenic for Pericardial effusion. | NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) VARIANT_IN_GENE NLRP3 → NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Pericardial effusion | {
"steps": [
{
"hop": 1,
"source_node_id": "NLRP3",
"source_node_type": "GENE",
"source_node_label": "NLRP3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_00124313... | NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NLRP3\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NLRP3\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg)",
"text": "NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) VARIANT_IN_GENE NLRP3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:pericardial_effusion",
"text": "NM_001243133.2(NLR... | {"gene": "NLRP3", "disease": "Pericardial effusion", "pathogenic_variants": ["NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg)"]} | 0.707107 | null |
no_dise_00276 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NF1 classified as Pathogenic or Likely Pathogenic for Neurofibromatosis-Noonan syndrome. | NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) VARIANT_IN_GENE NF1 → NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Neurofibromatosis-Noonan syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001042492.3(... | NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NF1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NF1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs)",
"text": "NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) VARIANT_IN_GENE NF1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:neurofibromatosis_noonan_syndrome",
"text": "N... | {"gene": "NF1", "disease": "Neurofibromatosis-Noonan syndrome", "pathogenic_variants": ["NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs)"]} | 0.83666 | null |
no_dise_00105 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BCL11B classified as Pathogenic or Likely Pathogenic for Combined immunodeficiency. | NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) VARIANT_IN_GENE BCL11B → NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Combined immunodeficiency | {
"steps": [
{
"hop": 1,
"source_node_id": "BCL11B",
"source_node_type": "GENE",
"source_node_label": "BCL11B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_138576... | NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BCL11B\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BCL11B\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys)",
"text": "NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) VARIANT_IN_GENE BCL11B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:combined_immunodeficiency",
"text": "NM_138576.4(BCL1... | {"gene": "BCL11B", "disease": "Combined immunodeficiency", "pathogenic_variants": ["NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys)"]} | 0.707107 | null |
no_dise_00285 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in APC classified as Pathogenic or Likely Pathogenic for Inherited polyposis and early onset colorectal cancer - germline testing. | NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) VARIANT_IN_GENE APC → NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited polyposis and early onset colorectal cancer - germline testing | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000038.6(APC... | NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"APC\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"APC\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_000038.6(APC):c.4175C>G (p.Ser1392Ter)",
"text": "NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_polyposis_and_early_onset_colorectal_cancer_germli",
... | {"gene": "APC", "disease": "Inherited polyposis and early onset colorectal cancer - germline testing", "pathogenic_variants": ["NM_000038.6(APC):c.4175C>G (p.Ser1392Ter)"]} | 0.83666 | null |
End of preview. Expand in Data Studio
Task types by split
| task_type | train | test |
|---|---|---|
disease_reasoning |
535 | 94 |
hallucination_detection |
668 | 132 |
interaction_propagation |
640 | 160 |
mechanistic_explanation |
610 | 190 |
path_traversal |
573 | 227 |
regulatory_reasoning |
672 | 128 |
Schema
Each item has:
id,task_type,pipeline(coding_variant/noncoding_regulatory),difficultyquestion,answer,choices(MCQ options, when applicable)context-- either a templated chain narration, or (ifllm_rewritewas applied) an LLM-rewritten fluent Step/Evidence/Interpretation/Conclusion narrativereasoning_chain-- the grounded, machine-checkable multi-hop path (steps: each withsource_node_id/target_node_id/edge_relation/edge_confidence/edge_source_db), never touched by any LLM stepmodality_data-- raw modality payloads (sequence, structural, transcriptomic, post_translational, signaling_role, etc.) attached to the chain's anchor nodesevidence-- supporting evidence entries with source database/PMIDpath_confidence_score-- continuous, confidence-derived difficulty score
Companion graph
graph.json (if included in this repo) is the exact knowledge graph these
items' reasoning_chain node IDs refer to -- load it with
GenBench's GraphBuilder.load() to
resolve full node/edge attributes beyond what's inlined in each item.
Source
Generated from GenBench:
train:data\hf_generated\splits_v6\train_noncoding.jsonltest:data\hf_generated\splits_v6\test_noncoding.jsonl
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