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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: 12-88506380-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=88506380&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 88506380,
"ref": "T",
"alt": "C",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "NM_000899.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.715-2A>G",
"hgvs_p": null,
"transcript": "NM_000899.5",
"protein_id": "NP_000890.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000644744.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000899.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.715-2A>G",
"hgvs_p": null,
"transcript": "ENST00000644744.1",
"protein_id": "ENSP00000495951.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000899.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644744.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.631-2A>G",
"hgvs_p": null,
"transcript": "ENST00000347404.10",
"protein_id": "ENSP00000054216.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 245,
"cds_start": null,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000347404.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "n.658-2A>G",
"hgvs_p": null,
"transcript": "ENST00000378535.4",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000378535.4"
},
{
"aa_ref": "Q",
"aa_alt": "R",
"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": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.737A>G",
"hgvs_p": "p.Gln246Arg",
"transcript": "ENST00000874530.1",
"protein_id": "ENSP00000544589.1",
"transcript_support_level": null,
"aa_start": 246,
"aa_end": null,
"aa_length": 281,
"cds_start": 737,
"cds_end": null,
"cds_length": 846,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874530.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.715-2A>G",
"hgvs_p": null,
"transcript": "ENST00000874529.1",
"protein_id": "ENSP00000544588.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874529.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.715-2A>G",
"hgvs_p": null,
"transcript": "ENST00000874531.1",
"protein_id": "ENSP00000544590.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874531.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.631-2A>G",
"hgvs_p": null,
"transcript": "NM_003994.6",
"protein_id": "NP_003985.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 245,
"cds_start": null,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003994.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.631-2A>G",
"hgvs_p": null,
"transcript": "ENST00000944532.1",
"protein_id": "ENSP00000614591.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 245,
"cds_start": null,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944532.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "c.64-2A>G",
"hgvs_p": null,
"transcript": "ENST00000357116.4",
"protein_id": "ENSP00000474021.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 56,
"cds_start": null,
"cds_end": null,
"cds_length": 171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357116.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"hgvs_c": "n.*716-2A>G",
"hgvs_p": null,
"transcript": "ENST00000646633.1",
"protein_id": "ENSP00000494139.1",
"transcript_support_level": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000646633.1"
}
],
"gene_symbol": "KITLG",
"gene_hgnc_id": 6343,
"dbsnp": "rs768146588",
"frequency_reference_population": 0.00006889545,
"hom_count_reference_population": 0,
"allele_count_reference_population": 110,
"gnomad_exomes_af": 0.0000699228,
"gnomad_genomes_af": 0.0000591436,
"gnomad_exomes_ac": 101,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10999999940395355,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9259999990463257,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.965,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.83,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999988247793601,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PP5,BS1_Supporting",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PVS1_Moderate",
"PP5",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000899.5",
"gene_symbol": "KITLG",
"hgnc_id": 6343,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AD,Unknown,AR",
"hgvs_c": "c.715-2A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal dominant nonsyndromic hearing loss 69,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:2",
"phenotype_combined": "Autosomal dominant nonsyndromic hearing loss 69|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}