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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: 16-31356698-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=31356698&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 31356698,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001286375.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "NM_000887.5",
"protein_id": "NP_000878.2",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 1163,
"cds_start": 217,
"cds_end": null,
"cds_length": 3492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000268296.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000887.5"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "ENST00000268296.9",
"protein_id": "ENSP00000268296.5",
"transcript_support_level": 1,
"aa_start": 73,
"aa_end": null,
"aa_length": 1163,
"cds_start": 217,
"cds_end": null,
"cds_length": 3492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000887.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000268296.9"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "ENST00000562522.2",
"protein_id": "ENSP00000454623.1",
"transcript_support_level": 1,
"aa_start": 73,
"aa_end": null,
"aa_length": 1169,
"cds_start": 217,
"cds_end": null,
"cds_length": 3510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000562522.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "n.284A>T",
"hgvs_p": null,
"transcript": "ENST00000567409.1",
"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": "retained_intron",
"feature": "ENST00000567409.1"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "NM_001286375.2",
"protein_id": "NP_001273304.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 1169,
"cds_start": 217,
"cds_end": null,
"cds_length": 3510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001286375.2"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "ENST00000958326.1",
"protein_id": "ENSP00000628385.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 1148,
"cds_start": 217,
"cds_end": null,
"cds_length": 3447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958326.1"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "ENST00000958327.1",
"protein_id": "ENSP00000628386.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 1047,
"cds_start": 217,
"cds_end": null,
"cds_length": 3144,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958327.1"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "ENST00000562918.5",
"protein_id": "ENSP00000483860.1",
"transcript_support_level": 2,
"aa_start": 73,
"aa_end": null,
"aa_length": 181,
"cds_start": 217,
"cds_end": null,
"cds_length": 546,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000562918.5"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "XM_047434074.1",
"protein_id": "XP_047290030.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 979,
"cds_start": 217,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434074.1"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "XM_011545852.2",
"protein_id": "XP_011544154.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 798,
"cds_start": 217,
"cds_end": null,
"cds_length": 2397,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011545852.2"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "XM_047434075.1",
"protein_id": "XP_047290031.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 627,
"cds_start": 217,
"cds_end": null,
"cds_length": 1884,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434075.1"
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser",
"transcript": "XM_011545854.2",
"protein_id": "XP_011544156.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 614,
"cds_start": 217,
"cds_end": null,
"cds_length": 1845,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011545854.2"
}
],
"gene_symbol": "ITGAX",
"gene_hgnc_id": 6152,
"dbsnp": "rs754538346",
"frequency_reference_population": 0.000010650135,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.00000900299,
"gnomad_genomes_af": 0.0000262709,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.033389657735824585,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.041,
"revel_prediction": "Benign",
"alphamissense_score": 0.0801,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.759,
"phylop100way_prediction": "Benign",
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001286375.2",
"gene_symbol": "ITGAX",
"hgnc_id": 6152,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.217A>T",
"hgvs_p": "p.Thr73Ser"
}
],
"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
}