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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: 6-31164800-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31164800&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31164800,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002701.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.884G>A",
"hgvs_p": "p.Arg295Gln",
"transcript": "NM_002701.6",
"protein_id": "NP_002692.2",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 360,
"cds_start": 884,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 1409,
"mane_select": "ENST00000259915.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.884G>A",
"hgvs_p": "p.Arg295Gln",
"transcript": "ENST00000259915.13",
"protein_id": "ENSP00000259915.7",
"transcript_support_level": 1,
"aa_start": 295,
"aa_end": null,
"aa_length": 360,
"cds_start": 884,
"cds_end": null,
"cds_length": 1083,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 1409,
"mane_select": "NM_002701.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.374G>A",
"hgvs_p": "p.Arg125Gln",
"transcript": "ENST00000606567.6",
"protein_id": "ENSP00000475880.2",
"transcript_support_level": 1,
"aa_start": 125,
"aa_end": null,
"aa_length": 190,
"cds_start": 374,
"cds_end": null,
"cds_length": 573,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 1236,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.296G>A",
"hgvs_p": "p.Arg99Gln",
"transcript": "ENST00000441888.7",
"protein_id": "ENSP00000389359.2",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 164,
"cds_start": 296,
"cds_end": null,
"cds_length": 495,
"cdna_start": 592,
"cdna_end": null,
"cdna_length": 1055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.296G>A",
"hgvs_p": "p.Arg99Gln",
"transcript": "ENST00000471529.6",
"protein_id": "ENSP00000425083.1",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 164,
"cds_start": 296,
"cds_end": null,
"cds_length": 495,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 1723,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.296G>A",
"hgvs_p": "p.Arg99Gln",
"transcript": "ENST00000512818.5",
"protein_id": "ENSP00000425479.1",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 164,
"cds_start": 296,
"cds_end": null,
"cds_length": 495,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 1233,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.296G>A",
"hgvs_p": "p.Arg99Gln",
"transcript": "ENST00000513407.1",
"protein_id": "ENSP00000475512.1",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 164,
"cds_start": 296,
"cds_end": null,
"cds_length": 495,
"cdna_start": 1827,
"cdna_end": null,
"cdna_length": 2276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.374G>A",
"hgvs_p": "p.Arg125Gln",
"transcript": "NM_001173531.3",
"protein_id": "NP_001167002.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 190,
"cds_start": 374,
"cds_end": null,
"cds_length": 573,
"cdna_start": 1116,
"cdna_end": null,
"cdna_length": 1579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.374G>A",
"hgvs_p": "p.Arg125Gln",
"transcript": "NM_203289.6",
"protein_id": "NP_976034.4",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 190,
"cds_start": 374,
"cds_end": null,
"cds_length": 573,
"cdna_start": 1602,
"cdna_end": null,
"cdna_length": 2065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"hgvs_c": "c.296G>A",
"hgvs_p": "p.Arg99Gln",
"transcript": "NM_001285986.2",
"protein_id": "NP_001272915.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 164,
"cds_start": 296,
"cds_end": null,
"cds_length": 495,
"cdna_start": 1827,
"cdna_end": null,
"cdna_length": 2290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "TCF19",
"gene_hgnc_id": 11629,
"hgvs_c": "c.798-1480C>T",
"hgvs_p": null,
"transcript": "ENST00000542218.2",
"protein_id": "ENSP00000439397.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 297,
"cds_start": -4,
"cds_end": null,
"cds_length": 894,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "POU5F1",
"gene_hgnc_id": 9221,
"dbsnp": "rs950764201",
"frequency_reference_population": 0.0000043405844,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000342351,
"gnomad_genomes_af": 0.0000131408,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.22980979084968567,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.314,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1077,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.45,
"phylop100way_prediction": "Uncertain_significance",
"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_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002701.6",
"gene_symbol": "POU5F1",
"hgnc_id": 9221,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.884G>A",
"hgvs_p": "p.Arg295Gln"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000542218.2",
"gene_symbol": "TCF19",
"hgnc_id": 11629,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.798-1480C>T",
"hgvs_p": null
}
],
"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
}