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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: X-108157002-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=108157002&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 108157002,
"ref": "A",
"alt": "C",
"effect": "stop_lost",
"transcript": "ENST00000334504.12",
"consequences": [
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5071T>G",
"hgvs_p": "p.Ter1691Gluext*?",
"transcript": "NM_033641.4",
"protein_id": "NP_378667.1",
"transcript_support_level": null,
"aa_start": 1691,
"aa_end": null,
"aa_length": 1690,
"cds_start": 5071,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 5297,
"cdna_end": null,
"cdna_length": 6685,
"mane_select": "ENST00000334504.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5071T>G",
"hgvs_p": "p.Ter1691Gluext*?",
"transcript": "ENST00000334504.12",
"protein_id": "ENSP00000334733.7",
"transcript_support_level": 5,
"aa_start": 1691,
"aa_end": null,
"aa_length": 1690,
"cds_start": 5071,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 5297,
"cdna_end": null,
"cdna_length": 6685,
"mane_select": "NM_033641.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5074T>G",
"hgvs_p": "p.Ter1692Gluext*?",
"transcript": "ENST00000372216.8",
"protein_id": "ENSP00000361290.4",
"transcript_support_level": 1,
"aa_start": 1692,
"aa_end": null,
"aa_length": 1691,
"cds_start": 5074,
"cds_end": null,
"cds_length": 5076,
"cdna_start": 5175,
"cdna_end": null,
"cdna_length": 6570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.4999T>G",
"hgvs_p": "p.Ter1667Gluext*?",
"transcript": "ENST00000621266.4",
"protein_id": "ENSP00000482970.1",
"transcript_support_level": 1,
"aa_start": 1667,
"aa_end": null,
"aa_length": 1666,
"cds_start": 4999,
"cds_end": null,
"cds_length": 5001,
"cdna_start": 5233,
"cdna_end": null,
"cdna_length": 6627,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.4900T>G",
"hgvs_p": "p.Ter1634Gluext*?",
"transcript": "ENST00000538570.5",
"protein_id": "ENSP00000445236.1",
"transcript_support_level": 1,
"aa_start": 1634,
"aa_end": null,
"aa_length": 1633,
"cds_start": 4900,
"cds_end": null,
"cds_length": 4902,
"cdna_start": 5134,
"cdna_end": null,
"cdna_length": 6528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5122T>G",
"hgvs_p": "p.Ter1708Gluext*?",
"transcript": "NM_001287758.2",
"protein_id": "NP_001274687.1",
"transcript_support_level": null,
"aa_start": 1708,
"aa_end": null,
"aa_length": 1707,
"cds_start": 5122,
"cds_end": null,
"cds_length": 5124,
"cdna_start": 5348,
"cdna_end": null,
"cdna_length": 6736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5122T>G",
"hgvs_p": "p.Ter1708Gluext*?",
"transcript": "ENST00000394872.6",
"protein_id": "ENSP00000378340.3",
"transcript_support_level": 5,
"aa_start": 1708,
"aa_end": null,
"aa_length": 1707,
"cds_start": 5122,
"cds_end": null,
"cds_length": 5124,
"cdna_start": 5356,
"cdna_end": null,
"cdna_length": 6750,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5074T>G",
"hgvs_p": "p.Ter1692Gluext*?",
"transcript": "NM_001847.4",
"protein_id": "NP_001838.2",
"transcript_support_level": null,
"aa_start": 1692,
"aa_end": null,
"aa_length": 1691,
"cds_start": 5074,
"cds_end": null,
"cds_length": 5076,
"cdna_start": 5161,
"cdna_end": null,
"cdna_length": 6549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.4999T>G",
"hgvs_p": "p.Ter1667Gluext*?",
"transcript": "NM_001287759.2",
"protein_id": "NP_001274688.1",
"transcript_support_level": null,
"aa_start": 1667,
"aa_end": null,
"aa_length": 1666,
"cds_start": 4999,
"cds_end": null,
"cds_length": 5001,
"cdna_start": 5225,
"cdna_end": null,
"cdna_length": 6613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.4900T>G",
"hgvs_p": "p.Ter1634Gluext*?",
"transcript": "NM_001287760.2",
"protein_id": "NP_001274689.1",
"transcript_support_level": null,
"aa_start": 1634,
"aa_end": null,
"aa_length": 1633,
"cds_start": 4900,
"cds_end": null,
"cds_length": 4902,
"cdna_start": 5126,
"cdna_end": null,
"cdna_length": 6514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 46,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5125T>G",
"hgvs_p": "p.Ter1709Gluext*?",
"transcript": "XM_006724617.4",
"protein_id": "XP_006724680.1",
"transcript_support_level": null,
"aa_start": 1709,
"aa_end": null,
"aa_length": 1708,
"cds_start": 5125,
"cds_end": null,
"cds_length": 5127,
"cdna_start": 5212,
"cdna_end": null,
"cdna_length": 6600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5053T>G",
"hgvs_p": "p.Ter1685Gluext*?",
"transcript": "XM_011530852.3",
"protein_id": "XP_011529154.1",
"transcript_support_level": null,
"aa_start": 1685,
"aa_end": null,
"aa_length": 1684,
"cds_start": 5053,
"cds_end": null,
"cds_length": 5055,
"cdna_start": 5140,
"cdna_end": null,
"cdna_length": 6528,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5041T>G",
"hgvs_p": "p.Ter1681Gluext*?",
"transcript": "XM_011530853.4",
"protein_id": "XP_011529155.1",
"transcript_support_level": null,
"aa_start": 1681,
"aa_end": null,
"aa_length": 1680,
"cds_start": 5041,
"cds_end": null,
"cds_length": 5043,
"cdna_start": 5957,
"cdna_end": null,
"cdna_length": 7345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"hgvs_c": "c.5002T>G",
"hgvs_p": "p.Ter1668Gluext*?",
"transcript": "XM_047441813.1",
"protein_id": "XP_047297769.1",
"transcript_support_level": null,
"aa_start": 1668,
"aa_end": null,
"aa_length": 1667,
"cds_start": 5002,
"cds_end": null,
"cds_length": 5004,
"cdna_start": 5089,
"cdna_end": null,
"cdna_length": 6477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A6",
"gene_hgnc_id": 2208,
"dbsnp": "rs769211787",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0.00000732495,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.33000001311302185,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"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": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.128,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM4,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM4",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000334504.12",
"gene_symbol": "COL4A6",
"hgnc_id": 2208,
"effects": [
"stop_lost"
],
"inheritance_mode": "XL",
"hgvs_c": "c.5071T>G",
"hgvs_p": "p.Ter1691Gluext*?"
}
],
"clinvar_disease": "COL4A6-related disorder,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "not provided|COL4A6-related disorder",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}