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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: 11-65641060-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=65641060&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 65641060,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006747.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "NM_006747.4",
"protein_id": "NP_006738.3",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 3499,
"mane_select": "ENST00000534313.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "ENST00000534313.6",
"protein_id": "ENSP00000436269.1",
"transcript_support_level": 1,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 312,
"cdna_end": null,
"cdna_length": 3499,
"mane_select": "NM_006747.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "ENST00000394224.4",
"protein_id": "ENSP00000377771.3",
"transcript_support_level": 1,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 435,
"cdna_end": null,
"cdna_length": 3640,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "NM_153253.30",
"protein_id": "NP_694985.29",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 435,
"cdna_end": null,
"cdna_length": 3622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "ENST00000527525.5",
"protein_id": "ENSP00000433686.1",
"transcript_support_level": 2,
"aa_start": 47,
"aa_end": null,
"aa_length": 940,
"cds_start": 139,
"cds_end": null,
"cds_length": 2823,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 3235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "ENST00000533361.1",
"protein_id": "ENSP00000436683.1",
"transcript_support_level": 4,
"aa_start": 47,
"aa_end": null,
"aa_length": 101,
"cds_start": 139,
"cds_end": null,
"cds_length": 308,
"cdna_start": 393,
"cdna_end": null,
"cdna_length": 562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_005274189.3",
"protein_id": "XP_005274246.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 386,
"cdna_end": null,
"cdna_length": 3573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_047427427.1",
"protein_id": "XP_047283383.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 2608,
"cdna_end": null,
"cdna_length": 5795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_047427428.1",
"protein_id": "XP_047283384.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 1381,
"cdna_end": null,
"cdna_length": 4568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_047427429.1",
"protein_id": "XP_047283385.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 3737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_047427430.1",
"protein_id": "XP_047283386.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 2846,
"cdna_end": null,
"cdna_length": 6033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_047427431.1",
"protein_id": "XP_047283387.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 1042,
"cds_start": 139,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 464,
"cdna_end": null,
"cdna_length": 3651,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_047427432.1",
"protein_id": "XP_047283388.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 789,
"cds_start": 139,
"cds_end": null,
"cds_length": 2370,
"cdna_start": 260,
"cdna_end": null,
"cdna_length": 2583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp",
"transcript": "XM_047427434.1",
"protein_id": "XP_047283390.1",
"transcript_support_level": null,
"aa_start": 47,
"aa_end": null,
"aa_length": 766,
"cds_start": 139,
"cds_end": null,
"cds_length": 2301,
"cdna_start": 260,
"cdna_end": null,
"cdna_length": 2599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"hgvs_c": "c.*120C>T",
"hgvs_p": null,
"transcript": "ENST00000526137.1",
"protein_id": "ENSP00000434362.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 5,
"cds_start": -4,
"cds_end": null,
"cds_length": 19,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SIPA1",
"gene_hgnc_id": 10885,
"dbsnp": "rs763573101",
"frequency_reference_population": 0.000033167165,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.000025593,
"gnomad_genomes_af": 0.000105085,
"gnomad_exomes_ac": 37,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07956841588020325,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.177,
"revel_prediction": "Benign",
"alphamissense_score": 0.1443,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.157,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_006747.4",
"gene_symbol": "SIPA1",
"hgnc_id": 10885,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Arg47Trp"
}
],
"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
}