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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: 1-31698605-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=31698605&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 31698605,
"ref": "T",
"alt": "A",
"effect": "stop_gained,splice_region_variant",
"transcript": "ENST00000373672.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "NM_001856.4",
"protein_id": "NP_001847.3",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1604,
"cds_start": 268,
"cds_end": null,
"cds_length": 4815,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5418,
"mane_select": "ENST00000373672.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 71,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "ENST00000373672.8",
"protein_id": "ENSP00000362776.3",
"transcript_support_level": 5,
"aa_start": 90,
"aa_end": null,
"aa_length": 1604,
"cds_start": 268,
"cds_end": null,
"cds_length": 4815,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5418,
"mane_select": "NM_001856.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.-246A>T",
"hgvs_p": null,
"transcript": "XM_047446439.1",
"protein_id": "XP_047302395.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1417,
"cds_start": -4,
"cds_end": null,
"cds_length": 4254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "ENST00000373668.7",
"protein_id": "ENSP00000362772.3",
"transcript_support_level": 2,
"aa_start": 90,
"aa_end": null,
"aa_length": 966,
"cds_start": 268,
"cds_end": null,
"cds_length": 2901,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 3643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_017000338.2",
"protein_id": "XP_016855827.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1593,
"cds_start": 268,
"cds_end": null,
"cds_length": 4782,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_017000339.2",
"protein_id": "XP_016855828.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1592,
"cds_start": 268,
"cds_end": null,
"cds_length": 4779,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5382,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_011540722.2",
"protein_id": "XP_011539024.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1589,
"cds_start": 268,
"cds_end": null,
"cds_length": 4770,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5373,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_005270481.2",
"protein_id": "XP_005270538.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1588,
"cds_start": 268,
"cds_end": null,
"cds_length": 4767,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5370,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_011540723.2",
"protein_id": "XP_011539025.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1573,
"cds_start": 268,
"cds_end": null,
"cds_length": 4722,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5325,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 70,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_011540724.2",
"protein_id": "XP_011539026.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1563,
"cds_start": 268,
"cds_end": null,
"cds_length": 4692,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5295,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_047446431.1",
"protein_id": "XP_047302387.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1561,
"cds_start": 268,
"cds_end": null,
"cds_length": 4686,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5289,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 69,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_047446432.1",
"protein_id": "XP_047302388.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1548,
"cds_start": 268,
"cds_end": null,
"cds_length": 4647,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_047446435.1",
"protein_id": "XP_047302391.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1520,
"cds_start": 268,
"cds_end": null,
"cds_length": 4563,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 5166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.-246A>T",
"hgvs_p": null,
"transcript": "XM_047446439.1",
"protein_id": "XP_047302395.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1417,
"cds_start": -4,
"cds_end": null,
"cds_length": 4254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 61,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_047446440.1",
"protein_id": "XP_047302396.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1270,
"cds_start": 268,
"cds_end": null,
"cds_length": 3813,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 4120,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_011540729.2",
"protein_id": "XP_011539031.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1068,
"cds_start": 268,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 3510,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*",
"transcript": "XM_011540730.2",
"protein_id": "XP_011539032.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 1052,
"cds_start": 268,
"cds_end": null,
"cds_length": 3159,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 3462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "n.419A>T",
"hgvs_p": null,
"transcript": "ENST00000532877.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "n.483A>T",
"hgvs_p": null,
"transcript": "XR_001736983.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2845,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"hgvs_c": "c.-246A>T",
"hgvs_p": null,
"transcript": "XM_047446439.1",
"protein_id": "XP_047302395.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1417,
"cds_start": -4,
"cds_end": null,
"cds_length": 4254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL16A1",
"gene_hgnc_id": 2193,
"dbsnp": "rs2228550",
"frequency_reference_population": 0.00002107283,
"hom_count_reference_population": 0,
"allele_count_reference_population": 34,
"gnomad_exomes_af": 0.0000218949,
"gnomad_genomes_af": 0.0000131647,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6200000047683716,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.44200000166893005,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.744,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0160831001593926,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000373672.8",
"gene_symbol": "COL16A1",
"hgnc_id": 2193,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.268A>T",
"hgvs_p": "p.Arg90*"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}