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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: 10-124401746-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=124401746&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 124401746,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000274.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "NM_000274.4",
"protein_id": "NP_000265.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1074,
"cdna_end": null,
"cdna_length": 2039,
"mane_select": "ENST00000368845.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "ENST00000368845.6",
"protein_id": "ENSP00000357838.5",
"transcript_support_level": 1,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1074,
"cdna_end": null,
"cdna_length": 2039,
"mane_select": "NM_000274.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met",
"transcript": "ENST00000539214.5",
"protein_id": "ENSP00000439042.1",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 301,
"cds_start": 580,
"cds_end": null,
"cds_length": 906,
"cdna_start": 899,
"cdna_end": null,
"cdna_length": 1864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "NM_001322965.2",
"protein_id": "NP_001309894.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1069,
"cdna_end": null,
"cdna_length": 2034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "NM_001322966.2",
"protein_id": "NP_001309895.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1389,
"cdna_end": null,
"cdna_length": 2354,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "NM_001322967.2",
"protein_id": "NP_001309896.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1194,
"cdna_end": null,
"cdna_length": 2159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "NM_001322968.2",
"protein_id": "NP_001309897.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1281,
"cdna_end": null,
"cdna_length": 2246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "NM_001322969.2",
"protein_id": "NP_001309898.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1161,
"cdna_end": null,
"cdna_length": 2126,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met",
"transcript": "NM_001322970.2",
"protein_id": "NP_001309899.1",
"transcript_support_level": null,
"aa_start": 332,
"aa_end": null,
"aa_length": 439,
"cds_start": 994,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 2342,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.673G>A",
"hgvs_p": "p.Val225Met",
"transcript": "NM_001322971.2",
"protein_id": "NP_001309900.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 332,
"cds_start": 673,
"cds_end": null,
"cds_length": 999,
"cdna_start": 753,
"cdna_end": null,
"cdna_length": 1718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met",
"transcript": "NM_001171814.2",
"protein_id": "NP_001165285.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 301,
"cds_start": 580,
"cds_end": null,
"cds_length": 906,
"cdna_start": 846,
"cdna_end": null,
"cdna_length": 1811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "c.394G>A",
"hgvs_p": "p.Val132Met",
"transcript": "NM_001322974.2",
"protein_id": "NP_001309903.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 239,
"cds_start": 394,
"cds_end": null,
"cds_length": 720,
"cdna_start": 960,
"cdna_end": null,
"cdna_length": 1925,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "n.795G>A",
"hgvs_p": null,
"transcript": "ENST00000467675.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 810,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"hgvs_c": "n.504G>A",
"hgvs_p": null,
"transcript": "ENST00000471127.1",
"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": 751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "OAT",
"gene_hgnc_id": 8091,
"dbsnp": "rs121965047",
"frequency_reference_population": 6.846989e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84699e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9796122312545776,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.821,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4267,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.753,
"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": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000274.4",
"gene_symbol": "OAT",
"hgnc_id": 8091,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.994G>A",
"hgvs_p": "p.Val332Met"
}
],
"clinvar_disease": "Gyrate atrophy of choroid and retina with pyridoxine-responsive ornithinemia,Ornithine aminotransferase deficiency",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"phenotype_combined": "Gyrate atrophy of choroid and retina with pyridoxine-responsive ornithinemia|Ornithine aminotransferase deficiency",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}