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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: 7-96121997-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=96121997&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 96121997,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000265631.10",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Gly531Asp",
"transcript": "NM_014251.3",
"protein_id": "NP_055066.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 675,
"cds_start": 1592,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 1734,
"cdna_end": null,
"cdna_length": 3141,
"mane_select": "ENST00000265631.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Gly531Asp",
"transcript": "ENST00000265631.10",
"protein_id": "ENSP00000265631.6",
"transcript_support_level": 1,
"aa_start": 531,
"aa_end": null,
"aa_length": 675,
"cds_start": 1592,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 1734,
"cdna_end": null,
"cdna_length": 3141,
"mane_select": "NM_014251.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "c.1595G>A",
"hgvs_p": "p.Gly532Asp",
"transcript": "ENST00000416240.6",
"protein_id": "ENSP00000400101.2",
"transcript_support_level": 1,
"aa_start": 532,
"aa_end": null,
"aa_length": 676,
"cds_start": 1595,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 1786,
"cdna_end": null,
"cdna_length": 3192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "c.1595G>A",
"hgvs_p": "p.Gly532Asp",
"transcript": "NM_001160210.2",
"protein_id": "NP_001153682.1",
"transcript_support_level": null,
"aa_start": 532,
"aa_end": null,
"aa_length": 676,
"cds_start": 1595,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 1737,
"cdna_end": null,
"cdna_length": 3144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "c.1730G>A",
"hgvs_p": "p.Gly577Asp",
"transcript": "XM_017011663.2",
"protein_id": "XP_016867152.2",
"transcript_support_level": null,
"aa_start": 577,
"aa_end": null,
"aa_length": 721,
"cds_start": 1730,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 1745,
"cdna_end": null,
"cdna_length": 3152,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "c.1625G>A",
"hgvs_p": "p.Gly542Asp",
"transcript": "XM_047419712.1",
"protein_id": "XP_047275668.1",
"transcript_support_level": null,
"aa_start": 542,
"aa_end": null,
"aa_length": 686,
"cds_start": 1625,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 1888,
"cdna_end": null,
"cdna_length": 3295,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "c.740G>A",
"hgvs_p": "p.Gly247Asp",
"transcript": "XM_047419715.1",
"protein_id": "XP_047275671.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 391,
"cds_start": 740,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 821,
"cdna_end": null,
"cdna_length": 2228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "n.2G>A",
"hgvs_p": null,
"transcript": "ENST00000494085.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"hgvs_c": "n.1618G>A",
"hgvs_p": null,
"transcript": "NR_027662.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3025,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC25A13",
"gene_hgnc_id": 10983,
"dbsnp": "rs80338724",
"frequency_reference_population": 0.0000054724205,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000547242,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9898688793182373,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8379999995231628,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.932,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9976,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.43,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.998765534772206,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000265631.10",
"gene_symbol": "SLC25A13",
"hgnc_id": 10983,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Gly531Asp"
}
],
"clinvar_disease": " adult-onset, type II,Citrin deficiency,Citrullinemia,Neonatal intrahepatic cholestasis due to citrin deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2 O:1",
"phenotype_combined": "Neonatal intrahepatic cholestasis due to citrin deficiency|Citrin deficiency|Citrullinemia|Citrullinemia, type II, adult-onset",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}