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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: 3-37533460-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=37533460&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 37533460,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002207.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "NM_002207.3",
"protein_id": "NP_002198.2",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 1035,
"cds_start": 1520,
"cds_end": null,
"cds_length": 3108,
"cdna_start": 1754,
"cdna_end": null,
"cdna_length": 7860,
"mane_select": "ENST00000264741.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002207.3"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "ENST00000264741.10",
"protein_id": "ENSP00000264741.5",
"transcript_support_level": 1,
"aa_start": 507,
"aa_end": null,
"aa_length": 1035,
"cds_start": 1520,
"cds_end": null,
"cds_length": 3108,
"cdna_start": 1754,
"cdna_end": null,
"cdna_length": 7860,
"mane_select": "NM_002207.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264741.10"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "ENST00000422441.5",
"protein_id": "ENSP00000397258.1",
"transcript_support_level": 1,
"aa_start": 507,
"aa_end": null,
"aa_length": 632,
"cds_start": 1520,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 1780,
"cdna_end": null,
"cdna_length": 2282,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000422441.5"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "ENST00000921363.1",
"protein_id": "ENSP00000591422.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 1034,
"cds_start": 1520,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 1677,
"cdna_end": null,
"cdna_length": 7780,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921363.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "ENST00000944256.1",
"protein_id": "ENSP00000614315.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 1034,
"cds_start": 1520,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 1752,
"cdna_end": null,
"cdna_length": 7855,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944256.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1511G>A",
"hgvs_p": "p.Gly504Glu",
"transcript": "ENST00000944258.1",
"protein_id": "ENSP00000614317.1",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 1032,
"cds_start": 1511,
"cds_end": null,
"cds_length": 3099,
"cdna_start": 1735,
"cdna_end": null,
"cdna_length": 4424,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944258.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "ENST00000944260.1",
"protein_id": "ENSP00000614319.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 1005,
"cds_start": 1520,
"cds_end": null,
"cds_length": 3018,
"cdna_start": 1752,
"cdna_end": null,
"cdna_length": 3583,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944260.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "ENST00000944257.1",
"protein_id": "ENSP00000614316.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 993,
"cds_start": 1520,
"cds_end": null,
"cds_length": 2982,
"cdna_start": 1722,
"cdna_end": null,
"cdna_length": 7696,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944257.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1382G>A",
"hgvs_p": "p.Gly461Glu",
"transcript": "ENST00000944261.1",
"protein_id": "ENSP00000614320.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 989,
"cds_start": 1382,
"cds_end": null,
"cds_length": 2970,
"cdna_start": 1459,
"cdna_end": null,
"cdna_length": 3382,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944261.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1382G>A",
"hgvs_p": "p.Gly461Glu",
"transcript": "ENST00000944259.1",
"protein_id": "ENSP00000614318.1",
"transcript_support_level": null,
"aa_start": 461,
"aa_end": null,
"aa_length": 988,
"cds_start": 1382,
"cds_end": null,
"cds_length": 2967,
"cdna_start": 1607,
"cdna_end": null,
"cdna_length": 3585,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944259.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu",
"transcript": "ENST00000921364.1",
"protein_id": "ENSP00000591423.1",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 961,
"cds_start": 1520,
"cds_end": null,
"cds_length": 2886,
"cdna_start": 1805,
"cdna_end": null,
"cdna_length": 3504,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921364.1"
}
],
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"dbsnp": "rs267561",
"frequency_reference_population": 0.5782655,
"hom_count_reference_population": 274594,
"allele_count_reference_population": 933021,
"gnomad_exomes_af": 0.580976,
"gnomad_genomes_af": 0.552207,
"gnomad_exomes_ac": 849080,
"gnomad_genomes_ac": 83941,
"gnomad_exomes_homalt": 250743,
"gnomad_genomes_homalt": 23851,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000017952218058781,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.268,
"revel_prediction": "Benign",
"alphamissense_score": 0.3638,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.878,
"phylop100way_prediction": "Pathogenic",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_002207.3",
"gene_symbol": "ITGA9",
"hgnc_id": 6145,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1520G>A",
"hgvs_p": "p.Gly507Glu"
}
],
"clinvar_disease": "ITGA9-related disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|ITGA9-related disorder|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}