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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: 19-40513498-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40513498&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40513498,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000598249.6",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*",
"transcript": "NM_020971.3",
"protein_id": "NP_066022.2",
"transcript_support_level": null,
"aa_start": 903,
"aa_end": null,
"aa_length": 2564,
"cds_start": 2709,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 3029,
"cdna_end": null,
"cdna_length": 8910,
"mane_select": "ENST00000598249.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*",
"transcript": "ENST00000598249.6",
"protein_id": "ENSP00000469242.1",
"transcript_support_level": 1,
"aa_start": 903,
"aa_end": null,
"aa_length": 2564,
"cds_start": 2709,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 3029,
"cdna_end": null,
"cdna_length": 8910,
"mane_select": "NM_020971.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*",
"transcript": "ENST00000352632.7",
"protein_id": "ENSP00000263373.2",
"transcript_support_level": 5,
"aa_start": 903,
"aa_end": null,
"aa_length": 2564,
"cds_start": 2709,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 2795,
"cdna_end": null,
"cdna_length": 8676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*",
"transcript": "ENST00000595535.5",
"protein_id": "ENSP00000470693.1",
"transcript_support_level": 5,
"aa_start": 903,
"aa_end": null,
"aa_length": 2002,
"cds_start": 2709,
"cds_end": null,
"cds_length": 6009,
"cdna_start": 2795,
"cdna_end": null,
"cdna_length": 6105,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*",
"transcript": "XM_017027049.2",
"protein_id": "XP_016882538.1",
"transcript_support_level": null,
"aa_start": 903,
"aa_end": null,
"aa_length": 2564,
"cds_start": 2709,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 3065,
"cdna_end": null,
"cdna_length": 8946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2367G>A",
"hgvs_p": "p.Trp789*",
"transcript": "XM_017027050.2",
"protein_id": "XP_016882539.1",
"transcript_support_level": null,
"aa_start": 789,
"aa_end": null,
"aa_length": 2450,
"cds_start": 2367,
"cds_end": null,
"cds_length": 7353,
"cdna_start": 2446,
"cdna_end": null,
"cdna_length": 8327,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*",
"transcript": "XM_017027051.2",
"protein_id": "XP_016882540.1",
"transcript_support_level": null,
"aa_start": 903,
"aa_end": null,
"aa_length": 2129,
"cds_start": 2709,
"cds_end": null,
"cds_length": 6390,
"cdna_start": 3029,
"cdna_end": null,
"cdna_length": 6943,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*",
"transcript": "XM_017027052.2",
"protein_id": "XP_016882541.1",
"transcript_support_level": null,
"aa_start": 903,
"aa_end": null,
"aa_length": 1309,
"cds_start": 2709,
"cds_end": null,
"cds_length": 3930,
"cdna_start": 3029,
"cdna_end": null,
"cdna_length": 4925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "n.885G>A",
"hgvs_p": null,
"transcript": "ENST00000597389.5",
"protein_id": "ENSP00000472136.1",
"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": 5957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"dbsnp": "rs864309618",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5400000214576721,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.54,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.678,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "ENST00000598249.6",
"gene_symbol": "SPTBN4",
"hgnc_id": 14896,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2709G>A",
"hgvs_p": "p.Trp903*"
}
],
"clinvar_disease": " and deafness, neuropathy,Neurodevelopmental disorder with hypotonia,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified|Neurodevelopmental disorder with hypotonia, neuropathy, and deafness",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}