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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: 4-48071561-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=48071561&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 48071561,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003328.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1471G>A",
"hgvs_p": "p.Ala491Thr",
"transcript": "NM_003328.3",
"protein_id": "NP_003319.2",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 527,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264316.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003328.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1471G>A",
"hgvs_p": "p.Ala491Thr",
"transcript": "ENST00000264316.9",
"protein_id": "ENSP00000264316.4",
"transcript_support_level": 1,
"aa_start": 491,
"aa_end": null,
"aa_length": 527,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003328.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264316.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "n.*68G>A",
"hgvs_p": null,
"transcript": "ENST00000514937.5",
"protein_id": "ENSP00000422139.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000514937.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "n.*68G>A",
"hgvs_p": null,
"transcript": "ENST00000514937.5",
"protein_id": "ENSP00000422139.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000514937.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1471G>A",
"hgvs_p": "p.Ala491Thr",
"transcript": "ENST00000506073.3",
"protein_id": "ENSP00000422798.2",
"transcript_support_level": 3,
"aa_start": 491,
"aa_end": null,
"aa_length": 527,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506073.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1189G>A",
"hgvs_p": "p.Ala397Thr",
"transcript": "ENST00000960124.1",
"protein_id": "ENSP00000630183.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 433,
"cds_start": 1189,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960124.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.436G>A",
"hgvs_p": "p.Ala146Thr",
"transcript": "ENST00000507351.1",
"protein_id": "ENSP00000423481.1",
"transcript_support_level": 2,
"aa_start": 146,
"aa_end": null,
"aa_length": 182,
"cds_start": 436,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000507351.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1480G>A",
"hgvs_p": "p.Ala494Thr",
"transcript": "XM_024454200.2",
"protein_id": "XP_024309968.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 530,
"cds_start": 1480,
"cds_end": null,
"cds_length": 1593,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024454200.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1414G>A",
"hgvs_p": "p.Ala472Thr",
"transcript": "XM_011513747.4",
"protein_id": "XP_011512049.1",
"transcript_support_level": null,
"aa_start": 472,
"aa_end": null,
"aa_length": 508,
"cds_start": 1414,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513747.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1396G>A",
"hgvs_p": "p.Ala466Thr",
"transcript": "XM_017008581.3",
"protein_id": "XP_016864070.1",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 502,
"cds_start": 1396,
"cds_end": null,
"cds_length": 1509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008581.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Ala350Thr",
"transcript": "XM_047416123.1",
"protein_id": "XP_047272079.1",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 386,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1161,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416123.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.757G>A",
"hgvs_p": "p.Ala253Thr",
"transcript": "XM_011513748.4",
"protein_id": "XP_011512050.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 289,
"cds_start": 757,
"cds_end": null,
"cds_length": 870,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513748.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "c.*68G>A",
"hgvs_p": null,
"transcript": "XM_047416122.1",
"protein_id": "XP_047272078.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 430,
"cds_start": null,
"cds_end": null,
"cds_length": 1293,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416122.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "n.*105G>A",
"hgvs_p": null,
"transcript": "ENST00000509681.1",
"protein_id": "ENSP00000424070.1",
"transcript_support_level": 3,
"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": "nonsense_mediated_decay",
"feature": "ENST00000509681.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"hgvs_c": "n.*105G>A",
"hgvs_p": null,
"transcript": "ENST00000509681.1",
"protein_id": "ENSP00000424070.1",
"transcript_support_level": 3,
"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": "nonsense_mediated_decay",
"feature": "ENST00000509681.1"
}
],
"gene_symbol": "TXK",
"gene_hgnc_id": 12434,
"dbsnp": "rs1188178413",
"frequency_reference_population": 0.00000681545,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000615659,
"gnomad_genomes_af": 0.0000131465,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9440616369247437,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.62,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2053,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.715,
"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,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_003328.3",
"gene_symbol": "TXK",
"hgnc_id": 12434,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1471G>A",
"hgvs_p": "p.Ala491Thr"
}
],
"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
}