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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: 6-87473010-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=87473010&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 87473010,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000369552.9",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.7G>A",
"hgvs_p": "p.Ala3Thr",
"transcript": "NM_006416.5",
"protein_id": "NP_006407.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 337,
"cds_start": 7,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 37,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": "ENST00000369552.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.7G>A",
"hgvs_p": "p.Ala3Thr",
"transcript": "ENST00000369552.9",
"protein_id": "ENSP00000358565.4",
"transcript_support_level": 1,
"aa_start": 3,
"aa_end": null,
"aa_length": 337,
"cds_start": 7,
"cds_end": null,
"cds_length": 1014,
"cdna_start": 37,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": "NM_006416.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.7G>A",
"hgvs_p": "p.Ala3Thr",
"transcript": "ENST00000369556.7",
"protein_id": "ENSP00000358569.3",
"transcript_support_level": 1,
"aa_start": 3,
"aa_end": null,
"aa_length": 278,
"cds_start": 7,
"cds_end": null,
"cds_length": 837,
"cdna_start": 86,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ENSG00000213204",
"gene_hgnc_id": null,
"hgvs_c": "n.*61-4352G>A",
"hgvs_p": null,
"transcript": "ENST00000507897.5",
"protein_id": "ENSP00000426769.1",
"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": 2301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.7G>A",
"hgvs_p": "p.Ala3Thr",
"transcript": "NM_001168398.2",
"protein_id": "NP_001161870.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 278,
"cds_start": 7,
"cds_end": null,
"cds_length": 837,
"cdna_start": 37,
"cdna_end": null,
"cdna_length": 1677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "c.7G>A",
"hgvs_p": "p.Ala3Thr",
"transcript": "ENST00000369557.9",
"protein_id": "ENSP00000358570.5",
"transcript_support_level": 2,
"aa_start": 3,
"aa_end": null,
"aa_length": 189,
"cds_start": 7,
"cds_end": null,
"cds_length": 570,
"cdna_start": 86,
"cdna_end": null,
"cdna_length": 1653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"hgvs_c": "n.91+2297G>A",
"hgvs_p": null,
"transcript": "ENST00000464978.5",
"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": 1299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000213204",
"gene_hgnc_id": null,
"hgvs_c": "n.556-4352G>A",
"hgvs_p": null,
"transcript": "ENST00000506888.5",
"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": 1842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000213204",
"gene_hgnc_id": null,
"hgvs_c": "n.510-4352G>A",
"hgvs_p": null,
"transcript": "ENST00000513191.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 583,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124901357",
"gene_hgnc_id": null,
"hgvs_c": "n.-65C>T",
"hgvs_p": null,
"transcript": "XR_007059668.1",
"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": 1222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC35A1",
"gene_hgnc_id": 11021,
"dbsnp": "rs149903512",
"frequency_reference_population": 0.000054247586,
"hom_count_reference_population": 0,
"allele_count_reference_population": 37,
"gnomad_exomes_af": 0.0000679448,
"gnomad_genomes_af": 0.00000656961,
"gnomad_exomes_ac": 36,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04144492745399475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.039,
"revel_prediction": "Benign",
"alphamissense_score": 0.117,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.137,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000369552.9",
"gene_symbol": "SLC35A1",
"hgnc_id": 11021,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7G>A",
"hgvs_p": "p.Ala3Thr"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000507897.5",
"gene_symbol": "ENSG00000213204",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*61-4352G>A",
"hgvs_p": null
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "XR_007059668.1",
"gene_symbol": "LOC124901357",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-65C>T",
"hgvs_p": null
}
],
"clinvar_disease": "SLC35A1-congenital disorder of glycosylation",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "SLC35A1-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}