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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: 3-37732740-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=37732740&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 37732740,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_002207.3",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2096T>A",
"hgvs_p": "p.Leu699Gln",
"transcript": "NM_002207.3",
"protein_id": "NP_002198.2",
"transcript_support_level": null,
"aa_start": 699,
"aa_end": null,
"aa_length": 1035,
"cds_start": 2096,
"cds_end": null,
"cds_length": 3108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264741.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002207.3"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2096T>A",
"hgvs_p": "p.Leu699Gln",
"transcript": "ENST00000264741.10",
"protein_id": "ENSP00000264741.5",
"transcript_support_level": 1,
"aa_start": 699,
"aa_end": null,
"aa_length": 1035,
"cds_start": 2096,
"cds_end": null,
"cds_length": 3108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002207.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264741.10"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2096T>A",
"hgvs_p": "p.Leu699Gln",
"transcript": "ENST00000921363.1",
"protein_id": "ENSP00000591422.1",
"transcript_support_level": null,
"aa_start": 699,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2096,
"cds_end": null,
"cds_length": 3105,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921363.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2093T>A",
"hgvs_p": "p.Leu698Gln",
"transcript": "ENST00000944256.1",
"protein_id": "ENSP00000614315.1",
"transcript_support_level": null,
"aa_start": 698,
"aa_end": null,
"aa_length": 1034,
"cds_start": 2093,
"cds_end": null,
"cds_length": 3105,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944256.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2087T>A",
"hgvs_p": "p.Leu696Gln",
"transcript": "ENST00000944258.1",
"protein_id": "ENSP00000614317.1",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 1032,
"cds_start": 2087,
"cds_end": null,
"cds_length": 3099,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944258.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2096T>A",
"hgvs_p": "p.Leu699Gln",
"transcript": "ENST00000944260.1",
"protein_id": "ENSP00000614319.1",
"transcript_support_level": null,
"aa_start": 699,
"aa_end": null,
"aa_length": 1005,
"cds_start": 2096,
"cds_end": null,
"cds_length": 3018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944260.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2096T>A",
"hgvs_p": "p.Leu699Gln",
"transcript": "ENST00000944257.1",
"protein_id": "ENSP00000614316.1",
"transcript_support_level": null,
"aa_start": 699,
"aa_end": null,
"aa_length": 993,
"cds_start": 2096,
"cds_end": null,
"cds_length": 2982,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944257.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1958T>A",
"hgvs_p": "p.Leu653Gln",
"transcript": "ENST00000944261.1",
"protein_id": "ENSP00000614320.1",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 989,
"cds_start": 1958,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944261.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.1958T>A",
"hgvs_p": "p.Leu653Gln",
"transcript": "ENST00000944259.1",
"protein_id": "ENSP00000614318.1",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 988,
"cds_start": 1958,
"cds_end": null,
"cds_length": 2967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944259.1"
},
{
"aa_ref": "L",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "c.2096T>A",
"hgvs_p": "p.Leu699Gln",
"transcript": "ENST00000921364.1",
"protein_id": "ENSP00000591423.1",
"transcript_support_level": null,
"aa_start": 699,
"aa_end": null,
"aa_length": 961,
"cds_start": 2096,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921364.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"hgvs_c": "n.169T>A",
"hgvs_p": null,
"transcript": "ENST00000461533.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000461533.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ITGA9-AS1",
"gene_hgnc_id": 49668,
"hgvs_c": "n.459+21189A>T",
"hgvs_p": null,
"transcript": "ENST00000653023.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000653023.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ITGA9-AS1",
"gene_hgnc_id": 49668,
"hgvs_c": "n.491-12321A>T",
"hgvs_p": null,
"transcript": "ENST00000653285.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000653285.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA9-AS1",
"gene_hgnc_id": 49668,
"hgvs_c": "n.290+16796A>T",
"hgvs_p": null,
"transcript": "ENST00000653850.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000653850.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ITGA9-AS1",
"gene_hgnc_id": 49668,
"hgvs_c": "n.408-12321A>T",
"hgvs_p": null,
"transcript": "ENST00000661580.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000661580.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ITGA9-AS1",
"gene_hgnc_id": 49668,
"hgvs_c": "n.405-12321A>T",
"hgvs_p": null,
"transcript": "ENST00000663533.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000663533.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ITGA9-AS1",
"gene_hgnc_id": 49668,
"hgvs_c": "n.452-4210A>T",
"hgvs_p": null,
"transcript": "ENST00000663634.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000663634.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ITGA9-AS1",
"gene_hgnc_id": 49668,
"hgvs_c": "n.536+5900A>T",
"hgvs_p": null,
"transcript": "ENST00000720827.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000720827.1"
}
],
"gene_symbol": "ITGA9",
"gene_hgnc_id": 6145,
"dbsnp": "rs917137238",
"frequency_reference_population": 0.0000020564426,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205644,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4218071699142456,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.172,
"revel_prediction": "Benign",
"alphamissense_score": 0.0809,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.452,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002207.3",
"gene_symbol": "ITGA9",
"hgnc_id": 6145,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2096T>A",
"hgvs_p": "p.Leu699Gln"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000653023.1",
"gene_symbol": "ITGA9-AS1",
"hgnc_id": 49668,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.459+21189A>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}