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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: 15-42399617-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=42399617&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PP4_Strong",
"PP3",
"PM3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CAPN3",
"hgnc_id": 1480,
"hgvs_c": "c.1319G>A",
"hgvs_p": "p.Arg440Gln",
"inheritance_mode": "AD,AR,SD",
"pathogenic_score": 9,
"score": 9,
"transcript": "NM_000070.3",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000258461",
"hgnc_id": null,
"hgvs_c": "n.*1115G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 13,
"score": 13,
"transcript": "ENST00000495723.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PP4_Strong,PP3,PM3_Strong",
"acmg_score": 9,
"allele_count_reference_population": 239,
"alphamissense_prediction": null,
"alphamissense_score": 0.4342,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.34,
"chr": "15",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": " autosomal dominant 4, limb-girdle,Abnormality of the musculature,Autosomal recessive limb-girdle muscular dystrophy,Autosomal recessive limb-girdle muscular dystrophy type 2A,Muscular dystrophy,not provided",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:10 LP:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.756389319896698,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 821,
"aa_ref": "R",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3315,
"cdna_start": 1624,
"cds_end": null,
"cds_length": 2466,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_000070.3",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "c.1319G>A",
"hgvs_p": "p.Arg440Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000397163.8",
"protein_coding": true,
"protein_id": "NP_000061.1",
"strand": true,
"transcript": "NM_000070.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 821,
"aa_ref": "R",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3315,
"cdna_start": 1624,
"cds_end": null,
"cds_length": 2466,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000397163.8",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "c.1319G>A",
"hgvs_p": "p.Arg440Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000070.3",
"protein_coding": true,
"protein_id": "ENSP00000380349.3",
"strand": true,
"transcript": "ENST00000397163.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 815,
"aa_ref": "R",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 1540,
"cds_end": null,
"cds_length": 2448,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000357568.8",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "c.1319G>A",
"hgvs_p": "p.Arg440Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000350181.3",
"strand": true,
"transcript": "ENST00000357568.8",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 729,
"aa_ref": "R",
"aa_start": 392,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3045,
"cdna_start": 1483,
"cds_end": null,
"cds_length": 2190,
"cds_start": 1175,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000349748.8",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "c.1175G>A",
"hgvs_p": "p.Arg392Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000183936.4",
"strand": true,
"transcript": "ENST00000349748.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 3881,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 26,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000495723.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1115G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000492063.1",
"strand": true,
"transcript": "ENST00000495723.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 3881,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 26,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000495723.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1115G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000492063.1",
"strand": true,
"transcript": "ENST00000495723.1",
"transcript_support_level": 2
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 815,
"aa_ref": "R",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3297,
"cdna_start": 1624,
"cds_end": null,
"cds_length": 2448,
"cds_start": 1319,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_024344.2",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "c.1319G>A",
"hgvs_p": "p.Arg440Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_077320.1",
"strand": true,
"transcript": "NM_024344.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 773,
"aa_ref": "R",
"aa_start": 392,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3172,
"cdna_start": 1481,
"cds_end": null,
"cds_length": 2322,
"cds_start": 1175,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000318023.11",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "c.1175G>A",
"hgvs_p": "p.Arg392Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000326281.8",
"strand": true,
"transcript": "ENST00000318023.11",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 729,
"aa_ref": "R",
"aa_start": 392,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3039,
"cdna_start": 1480,
"cds_end": null,
"cds_length": 2190,
"cds_start": 1175,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_173087.2",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "c.1175G>A",
"hgvs_p": "p.Arg392Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_775110.1",
"strand": true,
"transcript": "NM_173087.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3501,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 28,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000466369.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1393G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000492158.1",
"strand": true,
"transcript": "ENST00000466369.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3182,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000483208.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1115G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491847.1",
"strand": true,
"transcript": "ENST00000483208.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 27,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000549793.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1115G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491606.1",
"strand": true,
"transcript": "ENST00000549793.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2745,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000638141.2",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "n.1190G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000638141.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1166,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000673658.1",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "n.303G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000673658.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2239,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000673705.1",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "n.*19G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000501021.1",
"strand": true,
"transcript": "ENST00000673705.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3501,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 28,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000466369.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1393G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000492158.1",
"strand": true,
"transcript": "ENST00000466369.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3182,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 17,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000483208.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1115G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491847.1",
"strand": true,
"transcript": "ENST00000483208.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 27,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000549793.5",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000258461",
"hgvs_c": "n.*1115G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000491606.1",
"strand": true,
"transcript": "ENST00000549793.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2239,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000673705.1",
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"hgvs_c": "n.*19G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000501021.1",
"strand": true,
"transcript": "ENST00000673705.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376107921",
"effect": "missense_variant",
"frequency_reference_population": 0.00014834438,
"gene_hgnc_id": 1480,
"gene_symbol": "CAPN3",
"gnomad_exomes_ac": 214,
"gnomad_exomes_af": 0.000146684,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 25,
"gnomad_genomes_af": 0.000164262,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely pathogenic",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2A|not provided|Autosomal recessive limb-girdle muscular dystrophy type 2A;Muscular dystrophy, limb-girdle, autosomal dominant 4|Abnormality of the musculature|Muscular dystrophy, limb-girdle, autosomal dominant 4|Autosomal recessive limb-girdle muscular dystrophy",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.9,
"pos": 42399617,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.793,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_000070.3"
}
]
}