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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: 19-40570712-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40570712&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40570712,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000598249.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.7303C>T",
"hgvs_p": "p.Arg2435Cys",
"transcript": "NM_020971.3",
"protein_id": "NP_066022.2",
"transcript_support_level": null,
"aa_start": 2435,
"aa_end": null,
"aa_length": 2564,
"cds_start": 7303,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 7623,
"cdna_end": null,
"cdna_length": 8910,
"mane_select": "ENST00000598249.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.7303C>T",
"hgvs_p": "p.Arg2435Cys",
"transcript": "ENST00000598249.6",
"protein_id": "ENSP00000469242.1",
"transcript_support_level": 1,
"aa_start": 2435,
"aa_end": null,
"aa_length": 2564,
"cds_start": 7303,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 7623,
"cdna_end": null,
"cdna_length": 8910,
"mane_select": "NM_020971.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.7303C>T",
"hgvs_p": "p.Arg2435Cys",
"transcript": "ENST00000352632.7",
"protein_id": "ENSP00000263373.2",
"transcript_support_level": 5,
"aa_start": 2435,
"aa_end": null,
"aa_length": 2564,
"cds_start": 7303,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 7389,
"cdna_end": null,
"cdna_length": 8676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.7303C>T",
"hgvs_p": "p.Arg2435Cys",
"transcript": "XM_017027049.2",
"protein_id": "XP_016882538.1",
"transcript_support_level": null,
"aa_start": 2435,
"aa_end": null,
"aa_length": 2564,
"cds_start": 7303,
"cds_end": null,
"cds_length": 7695,
"cdna_start": 7659,
"cdna_end": null,
"cdna_length": 8946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "c.6961C>T",
"hgvs_p": "p.Arg2321Cys",
"transcript": "XM_017027050.2",
"protein_id": "XP_016882539.1",
"transcript_support_level": null,
"aa_start": 2321,
"aa_end": null,
"aa_length": 2450,
"cds_start": 6961,
"cds_end": null,
"cds_length": 7353,
"cdna_start": 7040,
"cdna_end": null,
"cdna_length": 8327,
"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": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "n.*3459C>T",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000301397",
"gene_hgnc_id": null,
"hgvs_c": "n.148G>A",
"hgvs_p": null,
"transcript": "ENST00000778634.1",
"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": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000301397",
"gene_hgnc_id": null,
"hgvs_c": "n.148G>A",
"hgvs_p": null,
"transcript": "ENST00000778635.1",
"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": 669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTBN4",
"gene_hgnc_id": 14896,
"hgvs_c": "n.*3459C>T",
"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": "rs777273785",
"frequency_reference_population": 0.000014301206,
"hom_count_reference_population": 0,
"allele_count_reference_population": 23,
"gnomad_exomes_af": 0.0000144231,
"gnomad_genomes_af": 0.0000131358,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0737026035785675,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.197,
"revel_prediction": "Benign",
"alphamissense_score": 0.5703,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.638,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "PP5,BP4",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000598249.6",
"gene_symbol": "SPTBN4",
"hgnc_id": 14896,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7303C>T",
"hgvs_p": "p.Arg2435Cys"
},
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000778634.1",
"gene_symbol": "ENSG00000301397",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.148G>A",
"hgvs_p": null
}
],
"clinvar_disease": " and deafness, neuropathy,Neurodevelopmental disorder with hypotonia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Neurodevelopmental disorder with hypotonia, neuropathy, and deafness",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}