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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: 16-15004210-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=15004210&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 15004210,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_015027.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "NM_015027.4",
"protein_id": "NP_055842.2",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 788,
"cds_start": 266,
"cds_end": null,
"cds_length": 2367,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000396410.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015027.4"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000396410.9",
"protein_id": "ENSP00000379691.4",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 788,
"cds_start": 266,
"cds_end": null,
"cds_length": 2367,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015027.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396410.9"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Gly62Asp",
"transcript": "ENST00000569715.5",
"protein_id": "ENSP00000455070.1",
"transcript_support_level": 1,
"aa_start": 62,
"aa_end": null,
"aa_length": 761,
"cds_start": 185,
"cds_end": null,
"cds_length": 2286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000569715.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000535621.6",
"protein_id": "ENSP00000437835.2",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 498,
"cds_start": 266,
"cds_end": null,
"cds_length": 1497,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000535621.6"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000957850.1",
"protein_id": "ENSP00000627909.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 816,
"cds_start": 266,
"cds_end": null,
"cds_length": 2451,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957850.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000881203.1",
"protein_id": "ENSP00000551262.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 815,
"cds_start": 266,
"cds_end": null,
"cds_length": 2448,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881203.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000881202.1",
"protein_id": "ENSP00000551261.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 810,
"cds_start": 266,
"cds_end": null,
"cds_length": 2433,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881202.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.320G>A",
"hgvs_p": "p.Gly107Asp",
"transcript": "ENST00000563679.5",
"protein_id": "ENSP00000454791.1",
"transcript_support_level": 2,
"aa_start": 107,
"aa_end": null,
"aa_length": 806,
"cds_start": 320,
"cds_end": null,
"cds_length": 2421,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000563679.5"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000881199.1",
"protein_id": "ENSP00000551258.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 806,
"cds_start": 266,
"cds_end": null,
"cds_length": 2421,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881199.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000881200.1",
"protein_id": "ENSP00000551259.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 797,
"cds_start": 266,
"cds_end": null,
"cds_length": 2394,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881200.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.263G>A",
"hgvs_p": "p.Gly88Asp",
"transcript": "NM_001324019.2",
"protein_id": "NP_001310948.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 787,
"cds_start": 263,
"cds_end": null,
"cds_length": 2364,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001324019.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.263G>A",
"hgvs_p": "p.Gly88Asp",
"transcript": "ENST00000881197.1",
"protein_id": "ENSP00000551256.1",
"transcript_support_level": null,
"aa_start": 88,
"aa_end": null,
"aa_length": 787,
"cds_start": 263,
"cds_end": null,
"cds_length": 2364,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881197.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000881198.1",
"protein_id": "ENSP00000551257.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 779,
"cds_start": 266,
"cds_end": null,
"cds_length": 2340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881198.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.221G>A",
"hgvs_p": "p.Gly74Asp",
"transcript": "NM_001285447.1",
"protein_id": "NP_001272376.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 773,
"cds_start": 221,
"cds_end": null,
"cds_length": 2322,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001285447.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000881204.1",
"protein_id": "ENSP00000551263.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 768,
"cds_start": 266,
"cds_end": null,
"cds_length": 2307,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881204.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Gly62Asp",
"transcript": "NM_001285444.2",
"protein_id": "NP_001272373.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 761,
"cds_start": 185,
"cds_end": null,
"cds_length": 2286,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001285444.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.182G>A",
"hgvs_p": "p.Gly61Asp",
"transcript": "NM_001285445.2",
"protein_id": "NP_001272374.1",
"transcript_support_level": null,
"aa_start": 61,
"aa_end": null,
"aa_length": 760,
"cds_start": 182,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001285445.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.182G>A",
"hgvs_p": "p.Gly61Asp",
"transcript": "ENST00000627450.2",
"protein_id": "ENSP00000486662.1",
"transcript_support_level": 2,
"aa_start": 61,
"aa_end": null,
"aa_length": 760,
"cds_start": 182,
"cds_end": null,
"cds_length": 2283,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000627450.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000940247.1",
"protein_id": "ENSP00000610306.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 759,
"cds_start": 266,
"cds_end": null,
"cds_length": 2280,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940247.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.185G>A",
"hgvs_p": "p.Gly62Asp",
"transcript": "ENST00000957851.1",
"protein_id": "ENSP00000627910.1",
"transcript_support_level": null,
"aa_start": 62,
"aa_end": null,
"aa_length": 752,
"cds_start": 185,
"cds_end": null,
"cds_length": 2259,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957851.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000940248.1",
"protein_id": "ENSP00000610307.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 737,
"cds_start": 266,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940248.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp",
"transcript": "ENST00000850604.1",
"protein_id": "ENSP00000520891.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 502,
"cds_start": 266,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
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{
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],
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{
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"feature": "NM_001285448.1"
},
{
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],
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"gene_symbol": "PDXDC1",
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"feature": "ENST00000450288.3"
},
{
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"protein_coding": false,
"strand": true,
"consequences": [
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],
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"feature": "ENST00000565362.5"
},
{
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"strand": true,
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"non_coding_transcript_exon_variant"
],
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{
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"consequences": [
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],
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000565362.5"
},
{
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"strand": true,
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"intron_variant"
],
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"gene_symbol": "PDXDC1",
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"hgvs_c": "n.174+2422G>A",
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"transcript": "ENST00000562119.5",
"protein_id": "ENSP00000455486.1",
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"cdna_start": null,
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"biotype": "nonsense_mediated_decay",
"feature": "ENST00000562119.5"
}
],
"gene_symbol": "PDXDC1",
"gene_hgnc_id": 28995,
"dbsnp": "rs545192333",
"frequency_reference_population": null,
"hom_count_reference_population": null,
"allele_count_reference_population": null,
"gnomad_exomes_af": 0.0000444721,
"gnomad_genomes_af": 0.0000656125,
"gnomad_exomes_ac": 65,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.12845617532730103,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.245,
"revel_prediction": "Benign",
"alphamissense_score": 0.6913,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.212,
"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": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_015027.4",
"gene_symbol": "PDXDC1",
"hgnc_id": 28995,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.266G>A",
"hgvs_p": "p.Gly89Asp"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}