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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 4-120695142-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=120695142&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 120695142,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001379104.1",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1862T>A",
"hgvs_p": "p.Met621Lys",
"transcript": "NM_018699.4",
"protein_id": "NP_061169.2",
"transcript_support_level": null,
"aa_start": 621,
"aa_end": null,
"aa_length": 630,
"cds_start": 1862,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1980,
"cdna_end": null,
"cdna_length": 5207,
"mane_select": "ENST00000264808.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018699.4"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1862T>A",
"hgvs_p": "p.Met621Lys",
"transcript": "ENST00000264808.8",
"protein_id": "ENSP00000264808.3",
"transcript_support_level": 1,
"aa_start": 621,
"aa_end": null,
"aa_length": 630,
"cds_start": 1862,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1980,
"cdna_end": null,
"cdna_length": 5207,
"mane_select": "NM_018699.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264808.8"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1769T>A",
"hgvs_p": "p.Met590Lys",
"transcript": "ENST00000428209.6",
"protein_id": "ENSP00000404832.2",
"transcript_support_level": 1,
"aa_start": 590,
"aa_end": null,
"aa_length": 599,
"cds_start": 1769,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 2019,
"cdna_end": null,
"cdna_length": 2338,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428209.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.*177T>A",
"hgvs_p": null,
"transcript": "ENST00000515109.5",
"protein_id": "ENSP00000422309.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 501,
"cds_start": null,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2259,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515109.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "n.2365T>A",
"hgvs_p": null,
"transcript": "ENST00000505484.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2396,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000505484.5"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1895T>A",
"hgvs_p": "p.Met632Lys",
"transcript": "NM_001379104.1",
"protein_id": "NP_001366033.1",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 641,
"cds_start": 1895,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 2013,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379104.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1895T>A",
"hgvs_p": "p.Met632Lys",
"transcript": "ENST00000940463.1",
"protein_id": "ENSP00000610522.1",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 641,
"cds_start": 1895,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 2293,
"cdna_end": null,
"cdna_length": 4001,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940463.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1802T>A",
"hgvs_p": "p.Met601Lys",
"transcript": "ENST00000940462.1",
"protein_id": "ENSP00000610521.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 610,
"cds_start": 1802,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 2043,
"cdna_end": null,
"cdna_length": 5265,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940462.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1769T>A",
"hgvs_p": "p.Met590Lys",
"transcript": "NM_001300823.2",
"protein_id": "NP_001287752.1",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 599,
"cds_start": 1769,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 1887,
"cdna_end": null,
"cdna_length": 5114,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001300823.2"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1757T>A",
"hgvs_p": "p.Met586Lys",
"transcript": "ENST00000898038.1",
"protein_id": "ENSP00000568097.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 595,
"cds_start": 1757,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1932,
"cdna_end": null,
"cdna_length": 5159,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898038.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1685T>A",
"hgvs_p": "p.Met562Lys",
"transcript": "ENST00000898039.1",
"protein_id": "ENSP00000568098.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 571,
"cds_start": 1685,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 1916,
"cdna_end": null,
"cdna_length": 2112,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898039.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1664T>A",
"hgvs_p": "p.Met555Lys",
"transcript": "NM_001379106.1",
"protein_id": "NP_001366035.1",
"transcript_support_level": null,
"aa_start": 555,
"aa_end": null,
"aa_length": 564,
"cds_start": 1664,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 1782,
"cdna_end": null,
"cdna_length": 5009,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379106.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1664T>A",
"hgvs_p": "p.Met555Lys",
"transcript": "ENST00000940461.1",
"protein_id": "ENSP00000610520.1",
"transcript_support_level": null,
"aa_start": 555,
"aa_end": null,
"aa_length": 564,
"cds_start": 1664,
"cds_end": null,
"cds_length": 1695,
"cdna_start": 2145,
"cdna_end": null,
"cdna_length": 5372,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940461.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1817T>A",
"hgvs_p": "p.Met606Lys",
"transcript": "XM_017007668.3",
"protein_id": "XP_016863157.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 615,
"cds_start": 1817,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 4638,
"cdna_end": null,
"cdna_length": 7865,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007668.3"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1802T>A",
"hgvs_p": "p.Met601Lys",
"transcript": "XM_011531563.3",
"protein_id": "XP_011529865.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 610,
"cds_start": 1802,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 1920,
"cdna_end": null,
"cdna_length": 5147,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531563.3"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1790T>A",
"hgvs_p": "p.Met597Lys",
"transcript": "XM_011531564.3",
"protein_id": "XP_011529866.1",
"transcript_support_level": null,
"aa_start": 597,
"aa_end": null,
"aa_length": 606,
"cds_start": 1790,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1908,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531564.3"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1757T>A",
"hgvs_p": "p.Met586Lys",
"transcript": "XM_047449554.1",
"protein_id": "XP_047305510.1",
"transcript_support_level": null,
"aa_start": 586,
"aa_end": null,
"aa_length": 595,
"cds_start": 1757,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 1875,
"cdna_end": null,
"cdna_length": 5102,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449554.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.920T>A",
"hgvs_p": "p.Met307Lys",
"transcript": "XM_017007671.2",
"protein_id": "XP_016863160.1",
"transcript_support_level": null,
"aa_start": 307,
"aa_end": null,
"aa_length": 316,
"cds_start": 920,
"cds_end": null,
"cds_length": 951,
"cdna_start": 1226,
"cdna_end": null,
"cdna_length": 4453,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007671.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.*177T>A",
"hgvs_p": null,
"transcript": "NM_001300824.2",
"protein_id": "NP_001287753.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 501,
"cds_start": null,
"cds_end": null,
"cds_length": 1506,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5028,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001300824.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1762-10117T>A",
"hgvs_p": null,
"transcript": "XM_011531566.4",
"protein_id": "XP_011529868.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 589,
"cds_start": null,
"cds_end": null,
"cds_length": 1770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2614,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531566.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1669-10117T>A",
"hgvs_p": null,
"transcript": "XM_047449557.1",
"protein_id": "XP_047305513.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 558,
"cds_start": null,
"cds_end": null,
"cds_length": 1677,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2521,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449557.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"hgvs_c": "c.1636-10117T>A",
"hgvs_p": null,
"transcript": "XM_047449558.1",
"protein_id": "XP_047305514.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 547,
"cds_start": null,
"cds_end": null,
"cds_length": 1644,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2488,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
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{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
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"gene_symbol": "PRDM5",
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"transcript": "ENST00000513741.1",
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"transcript_support_level": 5,
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"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
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"cdna_length": 210,
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"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000513741.1"
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{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
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"gene_symbol": "PRDM5",
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"hgvs_c": "n.*16T>A",
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"transcript": "ENST00000506065.1",
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"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 696,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000506065.1"
}
],
"gene_symbol": "PRDM5",
"gene_hgnc_id": 9349,
"dbsnp": "rs970486399",
"frequency_reference_population": 0.0000013688935,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.00000136889,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6948532462120056,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.298,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4536,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.15,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.947,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001379104.1",
"gene_symbol": "PRDM5",
"hgnc_id": 9349,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1895T>A",
"hgvs_p": "p.Met632Lys"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}