← Back to variant description
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: 15-42392678-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=42392678&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 42392678,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000397163.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "c.985G>C",
"hgvs_p": "p.Gly329Arg",
"transcript": "NM_000070.3",
"protein_id": "NP_000061.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 821,
"cds_start": 985,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 3315,
"mane_select": "ENST00000397163.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "c.985G>C",
"hgvs_p": "p.Gly329Arg",
"transcript": "ENST00000397163.8",
"protein_id": "ENSP00000380349.3",
"transcript_support_level": 1,
"aa_start": 329,
"aa_end": null,
"aa_length": 821,
"cds_start": 985,
"cds_end": null,
"cds_length": 2466,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 3315,
"mane_select": "NM_000070.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "c.985G>C",
"hgvs_p": "p.Gly329Arg",
"transcript": "ENST00000357568.8",
"protein_id": "ENSP00000350181.3",
"transcript_support_level": 1,
"aa_start": 329,
"aa_end": null,
"aa_length": 815,
"cds_start": 985,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 1206,
"cdna_end": null,
"cdna_length": 3130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "c.841G>C",
"hgvs_p": "p.Gly281Arg",
"transcript": "ENST00000349748.8",
"protein_id": "ENSP00000183936.4",
"transcript_support_level": 1,
"aa_start": 281,
"aa_end": null,
"aa_length": 729,
"cds_start": 841,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 3045,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*781G>C",
"hgvs_p": null,
"transcript": "ENST00000495723.1",
"protein_id": "ENSP00000492063.1",
"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": 3881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*781G>C",
"hgvs_p": null,
"transcript": "ENST00000495723.1",
"protein_id": "ENSP00000492063.1",
"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": 3881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "c.985G>C",
"hgvs_p": "p.Gly329Arg",
"transcript": "NM_024344.2",
"protein_id": "NP_077320.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 815,
"cds_start": 985,
"cds_end": null,
"cds_length": 2448,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 3297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "c.841G>C",
"hgvs_p": "p.Gly281Arg",
"transcript": "ENST00000318023.11",
"protein_id": "ENSP00000326281.8",
"transcript_support_level": 5,
"aa_start": 281,
"aa_end": null,
"aa_length": 773,
"cds_start": 841,
"cds_end": null,
"cds_length": 2322,
"cdna_start": 1147,
"cdna_end": null,
"cdna_length": 3172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "c.841G>C",
"hgvs_p": "p.Gly281Arg",
"transcript": "NM_173087.2",
"protein_id": "NP_775110.1",
"transcript_support_level": null,
"aa_start": 281,
"aa_end": null,
"aa_length": 729,
"cds_start": 841,
"cds_end": null,
"cds_length": 2190,
"cdna_start": 1146,
"cdna_end": null,
"cdna_length": 3039,
"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": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*1059G>C",
"hgvs_p": null,
"transcript": "ENST00000466369.5",
"protein_id": "ENSP00000492158.1",
"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": 3501,
"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": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*781G>C",
"hgvs_p": null,
"transcript": "ENST00000483208.5",
"protein_id": "ENSP00000491847.1",
"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": 3182,
"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": 11,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*781G>C",
"hgvs_p": null,
"transcript": "ENST00000549793.5",
"protein_id": "ENSP00000491606.1",
"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": 3223,
"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": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "n.856G>C",
"hgvs_p": null,
"transcript": "ENST00000638141.2",
"protein_id": null,
"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": 2745,
"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": 12,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*1059G>C",
"hgvs_p": null,
"transcript": "ENST00000466369.5",
"protein_id": "ENSP00000492158.1",
"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": 3501,
"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": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*781G>C",
"hgvs_p": null,
"transcript": "ENST00000483208.5",
"protein_id": "ENSP00000491847.1",
"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": 3182,
"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": 11,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258461",
"gene_hgnc_id": null,
"hgvs_c": "n.*781G>C",
"hgvs_p": null,
"transcript": "ENST00000549793.5",
"protein_id": "ENSP00000491606.1",
"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": 3223,
"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": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "n.71-4122G>C",
"hgvs_p": null,
"transcript": "ENST00000673705.1",
"protein_id": "ENSP00000501021.1",
"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": 2239,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"hgvs_c": "n.-32G>C",
"hgvs_p": null,
"transcript": "ENST00000673658.1",
"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": 1166,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CAPN3",
"gene_hgnc_id": 1480,
"dbsnp": "rs1085307995",
"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": 0.969326376914978,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.857,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9152,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.78,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS1_Very_Strong,PM1,PM2,PP3_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PS1_Very_Strong",
"PM1",
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000397163.8",
"gene_symbol": "CAPN3",
"hgnc_id": 1480,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.985G>C",
"hgvs_p": "p.Gly329Arg"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000495723.1",
"gene_symbol": "ENSG00000258461",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*781G>C",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal dominant 4, limb-girdle,Autosomal recessive limb-girdle muscular dystrophy type 2A,Muscular dystrophy",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2A|Muscular dystrophy, limb-girdle, autosomal dominant 4",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}