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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: 5-80813686-TC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=80813686&ref=TC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 80813686,
"ref": "TC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_002439.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2760delC",
"hgvs_p": "p.Tyr921fs",
"transcript": "NM_002439.5",
"protein_id": "NP_002430.3",
"transcript_support_level": null,
"aa_start": 920,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2760,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 2836,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": "ENST00000265081.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002439.5"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2760delC",
"hgvs_p": "p.Tyr921fs",
"transcript": "ENST00000265081.7",
"protein_id": "ENSP00000265081.6",
"transcript_support_level": 1,
"aa_start": 920,
"aa_end": null,
"aa_length": 1137,
"cds_start": 2760,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 2836,
"cdna_end": null,
"cdna_length": 4443,
"mane_select": "NM_002439.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000265081.7"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2592delC",
"hgvs_p": "p.Tyr865fs",
"transcript": "ENST00000658259.1",
"protein_id": "ENSP00000499617.1",
"transcript_support_level": null,
"aa_start": 864,
"aa_end": null,
"aa_length": 1081,
"cds_start": 2592,
"cds_end": null,
"cds_length": 3246,
"cdna_start": 2634,
"cdna_end": null,
"cdna_length": 3295,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000658259.1"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2565delC",
"hgvs_p": "p.Tyr856fs",
"transcript": "ENST00000667069.1",
"protein_id": "ENSP00000499502.1",
"transcript_support_level": null,
"aa_start": 855,
"aa_end": null,
"aa_length": 1072,
"cds_start": 2565,
"cds_end": null,
"cds_length": 3219,
"cdna_start": 2599,
"cdna_end": null,
"cdna_length": 3964,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000667069.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.2760delC",
"hgvs_p": null,
"transcript": "ENST00000670357.1",
"protein_id": "ENSP00000499791.1",
"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": 4486,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000670357.1"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2760delC",
"hgvs_p": "p.Tyr921fs",
"transcript": "ENST00000875834.1",
"protein_id": "ENSP00000545893.1",
"transcript_support_level": null,
"aa_start": 920,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2760,
"cds_end": null,
"cds_length": 3477,
"cdna_start": 2838,
"cdna_end": null,
"cdna_length": 4840,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875834.1"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2664delC",
"hgvs_p": "p.Tyr889fs",
"transcript": "ENST00000969134.1",
"protein_id": "ENSP00000639193.1",
"transcript_support_level": null,
"aa_start": 888,
"aa_end": null,
"aa_length": 1105,
"cds_start": 2664,
"cds_end": null,
"cds_length": 3318,
"cdna_start": 2709,
"cdna_end": null,
"cdna_length": 3420,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969134.1"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2517delC",
"hgvs_p": "p.Tyr840fs",
"transcript": "ENST00000875835.1",
"protein_id": "ENSP00000545894.1",
"transcript_support_level": null,
"aa_start": 839,
"aa_end": null,
"aa_length": 1056,
"cds_start": 2517,
"cds_end": null,
"cds_length": 3171,
"cdna_start": 2558,
"cdna_end": null,
"cdna_length": 4165,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875835.1"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2448delC",
"hgvs_p": "p.Tyr817fs",
"transcript": "ENST00000933917.1",
"protein_id": "ENSP00000603976.1",
"transcript_support_level": null,
"aa_start": 816,
"aa_end": null,
"aa_length": 1033,
"cds_start": 2448,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 2522,
"cdna_end": null,
"cdna_length": 3237,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000933917.1"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.2001delC",
"hgvs_p": "p.Tyr668fs",
"transcript": "ENST00000875836.1",
"protein_id": "ENSP00000545895.1",
"transcript_support_level": null,
"aa_start": 667,
"aa_end": null,
"aa_length": 884,
"cds_start": 2001,
"cds_end": null,
"cds_length": 2655,
"cdna_start": 2077,
"cdna_end": null,
"cdna_length": 2759,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875836.1"
},
{
"aa_ref": "S",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "c.1788delC",
"hgvs_p": "p.Tyr597fs",
"transcript": "ENST00000969133.1",
"protein_id": "ENSP00000639192.1",
"transcript_support_level": null,
"aa_start": 596,
"aa_end": null,
"aa_length": 813,
"cds_start": 1788,
"cds_end": null,
"cds_length": 2442,
"cdna_start": 1841,
"cdna_end": null,
"cdna_length": 3261,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969133.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"hgvs_c": "n.63delC",
"hgvs_p": null,
"transcript": "ENST00000659302.1",
"protein_id": "ENSP00000499680.1",
"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": 1570,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000659302.1"
}
],
"gene_symbol": "MSH3",
"gene_hgnc_id": 7326,
"dbsnp": "rs751326348",
"frequency_reference_population": 0.0000068153317,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000547246,
"gnomad_genomes_af": 0.0000197184,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.102,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_002439.5",
"gene_symbol": "MSH3",
"hgnc_id": 7326,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2760delC",
"hgvs_p": "p.Tyr921fs"
}
],
"clinvar_disease": "Endometrial carcinoma,Familial adenomatous polyposis 4,Hereditary cancer-predisposing syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:8 LP:1",
"phenotype_combined": "Familial adenomatous polyposis 4|not provided|Endometrial carcinoma|Endometrial carcinoma;Familial adenomatous polyposis 4|Hereditary cancer-predisposing syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}