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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: 16-2046238-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=2046238&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 2046238,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000651570.2",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Gln82*",
"transcript": "NM_002528.7",
"protein_id": "NP_002519.2",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 304,
"cds_start": 244,
"cds_end": null,
"cds_length": 915,
"cdna_start": 255,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": "ENST00000651570.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Gln82*",
"transcript": "ENST00000651570.2",
"protein_id": "ENSP00000498421.1",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 304,
"cds_start": 244,
"cds_end": null,
"cds_length": 915,
"cdna_start": 255,
"cdna_end": null,
"cdna_length": 1030,
"mane_select": "NM_002528.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Gln90*",
"transcript": "ENST00000219066.5",
"protein_id": "ENSP00000219066.1",
"transcript_support_level": 1,
"aa_start": 90,
"aa_end": null,
"aa_length": 312,
"cds_start": 268,
"cds_end": null,
"cds_length": 939,
"cdna_start": 287,
"cdna_end": null,
"cdna_length": 1067,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Gln82*",
"transcript": "NM_001318193.2",
"protein_id": "NP_001305122.2",
"transcript_support_level": null,
"aa_start": 82,
"aa_end": null,
"aa_length": 247,
"cds_start": 244,
"cds_end": null,
"cds_length": 744,
"cdna_start": 255,
"cdna_end": null,
"cdna_length": 859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.205C>T",
"hgvs_p": "p.Gln69*",
"transcript": "ENST00000566380.5",
"protein_id": "ENSP00000455267.1",
"transcript_support_level": 3,
"aa_start": 69,
"aa_end": null,
"aa_length": 235,
"cds_start": 205,
"cds_end": null,
"cds_length": 708,
"cdna_start": 207,
"cdna_end": null,
"cdna_length": 814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.199C>T",
"hgvs_p": "p.Gln67*",
"transcript": "ENST00000651583.1",
"protein_id": "ENSP00000498821.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 232,
"cds_start": 199,
"cds_end": null,
"cds_length": 699,
"cdna_start": 199,
"cdna_end": null,
"cdna_length": 802,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.163C>T",
"hgvs_p": null,
"transcript": "ENST00000561841.1",
"protein_id": "ENSP00000456301.1",
"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": 1052,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.-36C>T",
"hgvs_p": null,
"transcript": "XM_047434171.1",
"protein_id": "XP_047290127.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 211,
"cds_start": -4,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.24+42C>T",
"hgvs_p": null,
"transcript": "NM_001318194.2",
"protein_id": "NP_001305123.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 194,
"cds_start": -4,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.172+42C>T",
"hgvs_p": null,
"transcript": "ENST00000568513.5",
"protein_id": "ENSP00000457818.1",
"transcript_support_level": 3,
"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": 837,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "c.-48C>T",
"hgvs_p": null,
"transcript": "ENST00000651522.1",
"protein_id": "ENSP00000498290.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 208,
"cds_start": -4,
"cds_end": null,
"cds_length": 627,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"hgvs_c": "n.-24C>T",
"hgvs_p": null,
"transcript": "ENST00000562120.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NTHL1",
"gene_hgnc_id": 8028,
"dbsnp": "rs150766139",
"frequency_reference_population": 0.0015918671,
"hom_count_reference_population": 1,
"allele_count_reference_population": 2568,
"gnomad_exomes_af": 0.00161813,
"gnomad_genomes_af": 0.00133985,
"gnomad_exomes_ac": 2364,
"gnomad_genomes_ac": 204,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.28999999165534973,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.67,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.18,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PVS1",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000651570.2",
"gene_symbol": "NTHL1",
"hgnc_id": 8028,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.244C>T",
"hgvs_p": "p.Gln82*"
}
],
"clinvar_disease": "Familial adenomatous polyposis 3,Hereditary cancer-predisposing syndrome,Inherited polyposis and early onset colorectal cancer - germline testing,NTHL1-related disorder,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:26 LP:1 US:1 O:1",
"phenotype_combined": "Familial adenomatous polyposis 3|Hereditary cancer-predisposing syndrome|NTHL1-related disorder|Inherited polyposis and early onset colorectal cancer - germline testing|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}