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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: 7-96121733-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=96121733&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP2",
"PP3_Strong",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC25A13",
"hgnc_id": 10983,
"hgvs_c": "c.1766G>A",
"hgvs_p": "p.Arg589Gln",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_001160210.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PP2,PP3_Strong,PP5",
"acmg_score": 12,
"allele_count_reference_population": 11,
"alphamissense_prediction": null,
"alphamissense_score": 0.9869,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.37,
"chr": "7",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Citrin deficiency,Citrullinemia,Citrullinemia type II,Inborn genetic diseases,Neonatal intrahepatic cholestasis due to citrin deficiency,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:2 US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9621298909187317,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 675,
"aa_ref": "R",
"aa_start": 588,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3141,
"cdna_start": 1905,
"cds_end": null,
"cds_length": 2028,
"cds_start": 1763,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_014251.3",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1763G>A",
"hgvs_p": "p.Arg588Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265631.10",
"protein_coding": true,
"protein_id": "NP_055066.1",
"strand": false,
"transcript": "NM_014251.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 675,
"aa_ref": "R",
"aa_start": 588,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3141,
"cdna_start": 1905,
"cds_end": null,
"cds_length": 2028,
"cds_start": 1763,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000265631.10",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1763G>A",
"hgvs_p": "p.Arg588Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014251.3",
"protein_coding": true,
"protein_id": "ENSP00000265631.6",
"strand": false,
"transcript": "ENST00000265631.10",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 676,
"aa_ref": "R",
"aa_start": 589,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3192,
"cdna_start": 1957,
"cds_end": null,
"cds_length": 2031,
"cds_start": 1766,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000416240.6",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1766G>A",
"hgvs_p": "p.Arg589Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000400101.2",
"strand": false,
"transcript": "ENST00000416240.6",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 715,
"aa_ref": "R",
"aa_start": 628,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3261,
"cdna_start": 2026,
"cds_end": null,
"cds_length": 2148,
"cds_start": 1883,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000856215.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1883G>A",
"hgvs_p": "p.Arg628Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526274.1",
"strand": false,
"transcript": "ENST00000856215.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 694,
"aa_ref": "R",
"aa_start": 607,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2965,
"cdna_start": 1924,
"cds_end": null,
"cds_length": 2085,
"cds_start": 1820,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "ENST00000856219.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1820G>A",
"hgvs_p": "p.Arg607Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526278.1",
"strand": false,
"transcript": "ENST00000856219.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 676,
"aa_ref": "R",
"aa_start": 589,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3144,
"cdna_start": 1908,
"cds_end": null,
"cds_length": 2031,
"cds_start": 1766,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_001160210.2",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1766G>A",
"hgvs_p": "p.Arg589Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001153682.1",
"strand": false,
"transcript": "NM_001160210.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 674,
"aa_ref": "R",
"aa_start": 587,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3164,
"cdna_start": 1929,
"cds_end": null,
"cds_length": 2025,
"cds_start": 1760,
"consequences": [
"missense_variant"
],
"exon_count": 18,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000948397.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1760G>A",
"hgvs_p": "p.Arg587Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618456.1",
"strand": false,
"transcript": "ENST00000948397.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 657,
"aa_ref": "R",
"aa_start": 570,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3074,
"cdna_start": 1841,
"cds_end": null,
"cds_length": 1974,
"cds_start": 1709,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000856217.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1709G>A",
"hgvs_p": "p.Arg570Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526276.1",
"strand": false,
"transcript": "ENST00000856217.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 648,
"aa_ref": "R",
"aa_start": 561,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3054,
"cdna_start": 1818,
"cds_end": null,
"cds_length": 1947,
"cds_start": 1682,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000856216.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1682G>A",
"hgvs_p": "p.Arg561Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526275.1",
"strand": false,
"transcript": "ENST00000856216.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 628,
"aa_ref": "R",
"aa_start": 541,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2952,
"cdna_start": 1714,
"cds_end": null,
"cds_length": 1887,
"cds_start": 1622,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000856218.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1622G>A",
"hgvs_p": "p.Arg541Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526277.1",
"strand": false,
"transcript": "ENST00000856218.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 622,
"aa_ref": "R",
"aa_start": 535,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2978,
"cdna_start": 1742,
"cds_end": null,
"cds_length": 1869,
"cds_start": 1604,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000935610.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1604G>A",
"hgvs_p": "p.Arg535Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000605669.1",
"strand": false,
"transcript": "ENST00000935610.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 610,
"aa_ref": "R",
"aa_start": 523,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2705,
"cdna_start": 1663,
"cds_end": null,
"cds_length": 1833,
"cds_start": 1568,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000856220.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1568G>A",
"hgvs_p": "p.Arg523Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526279.1",
"strand": false,
"transcript": "ENST00000856220.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 394,
"aa_ref": "R",
"aa_start": 307,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2320,
"cdna_start": 1084,
"cds_end": null,
"cds_length": 1185,
"cds_start": 920,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000856214.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.920G>A",
"hgvs_p": "p.Arg307Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000526273.1",
"strand": false,
"transcript": "ENST00000856214.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 721,
"aa_ref": "R",
"aa_start": 634,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3152,
"cdna_start": 1916,
"cds_end": null,
"cds_length": 2166,
"cds_start": 1901,
"consequences": [
"missense_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_017011663.2",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1901G>A",
"hgvs_p": "p.Arg634Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016867152.2",
"strand": false,
"transcript": "XM_017011663.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 686,
"aa_ref": "R",
"aa_start": 599,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3295,
"cdna_start": 2059,
"cds_end": null,
"cds_length": 2061,
"cds_start": 1796,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 18,
"exon_rank_end": null,
"feature": "XM_047419712.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.1796G>A",
"hgvs_p": "p.Arg599Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275668.1",
"strand": false,
"transcript": "XM_047419712.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 391,
"aa_ref": "R",
"aa_start": 304,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2228,
"cdna_start": 992,
"cds_end": null,
"cds_length": 1176,
"cds_start": 911,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047419715.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "c.911G>A",
"hgvs_p": "p.Arg304Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047275671.1",
"strand": false,
"transcript": "XM_047419715.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 766,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000494085.1",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "n.266G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000494085.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3025,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NR_027662.2",
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"hgvs_c": "n.1789G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_027662.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs121908532",
"effect": "missense_variant",
"frequency_reference_population": 0.0000075246603,
"gene_hgnc_id": 10983,
"gene_symbol": "SLC25A13",
"gnomad_exomes_ac": 11,
"gnomad_exomes_af": 0.00000752466,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Citrullinemia type II|not provided|Citrullinemia|Neonatal intrahepatic cholestasis due to citrin deficiency|Inborn genetic diseases|Citrin deficiency",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.687,
"pos": 96121733,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.832,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.23000000417232513,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.23,
"transcript": "NM_001160210.2"
}
]
}