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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: 4-140395849-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=140395849&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 140395849,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_004362.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "NM_004362.3",
"protein_id": "NP_004353.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 610,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000325617.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004362.3"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "ENST00000325617.10",
"protein_id": "ENSP00000326699.5",
"transcript_support_level": 1,
"aa_start": 373,
"aa_end": null,
"aa_length": 610,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004362.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000325617.10"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "ENST00000414773.5",
"protein_id": "ENSP00000392782.1",
"transcript_support_level": 1,
"aa_start": 373,
"aa_end": null,
"aa_length": 610,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000414773.5"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "NM_001130675.2",
"protein_id": "NP_001124147.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 610,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130675.2"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "ENST00000897460.1",
"protein_id": "ENSP00000567519.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 610,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000897460.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "ENST00000931054.1",
"protein_id": "ENSP00000601113.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 610,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931054.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "ENST00000931055.1",
"protein_id": "ENSP00000601114.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 610,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1833,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000931055.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "ENST00000963782.1",
"protein_id": "ENSP00000633841.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 609,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963782.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser",
"transcript": "ENST00000963785.1",
"protein_id": "ENSP00000633844.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 609,
"cds_start": 1119,
"cds_end": null,
"cds_length": 1830,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963785.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.951A>T",
"hgvs_p": "p.Arg317Ser",
"transcript": "ENST00000963784.1",
"protein_id": "ENSP00000633843.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 554,
"cds_start": 951,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963784.1"
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"hgvs_c": "c.654A>T",
"hgvs_p": "p.Arg218Ser",
"transcript": "ENST00000963783.1",
"protein_id": "ENSP00000633842.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 455,
"cds_start": 654,
"cds_end": null,
"cds_length": 1368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000963783.1"
}
],
"gene_symbol": "CLGN",
"gene_hgnc_id": 2060,
"dbsnp": "rs377332621",
"frequency_reference_population": 0.000055653418,
"hom_count_reference_population": 0,
"allele_count_reference_population": 86,
"gnomad_exomes_af": 0.0000559865,
"gnomad_genomes_af": 0.0000526025,
"gnomad_exomes_ac": 78,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07336226105690002,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.092,
"revel_prediction": "Benign",
"alphamissense_score": 0.2204,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.014,
"phylop100way_prediction": "Benign",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004362.3",
"gene_symbol": "CLGN",
"hgnc_id": 2060,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1119A>T",
"hgvs_p": "p.Arg373Ser"
}
],
"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
}