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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: 2-30738257-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=30738257&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 30738257,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_144575.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "NM_144575.3",
"protein_id": "NP_653176.2",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295055.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_144575.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "ENST00000295055.12",
"protein_id": "ENSP00000295055.8",
"transcript_support_level": 5,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_144575.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295055.12"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "ENST00000946473.1",
"protein_id": "ENSP00000616532.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946473.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "ENST00000946475.1",
"protein_id": "ENSP00000616534.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946475.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "ENST00000946477.1",
"protein_id": "ENSP00000616536.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946477.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"transcript": "ENST00000946472.1",
"protein_id": "ENSP00000616531.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 665,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1998,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946472.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1592G>A",
"hgvs_p": "p.Arg531His",
"transcript": "ENST00000946476.1",
"protein_id": "ENSP00000616535.1",
"transcript_support_level": null,
"aa_start": 531,
"aa_end": null,
"aa_length": 656,
"cds_start": 1592,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946476.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1556G>A",
"hgvs_p": "p.Arg519His",
"transcript": "ENST00000946474.1",
"protein_id": "ENSP00000616533.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 644,
"cds_start": 1556,
"cds_end": null,
"cds_length": 1935,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000946474.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "XM_011533159.4",
"protein_id": "XP_011531461.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533159.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "XM_011533160.3",
"protein_id": "XP_011531462.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533160.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "XM_011533161.4",
"protein_id": "XP_011531463.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011533161.4"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His",
"transcript": "XM_047446332.1",
"protein_id": "XP_047302288.1",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 669,
"cds_start": 1631,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047446332.1"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "c.1619G>A",
"hgvs_p": "p.Arg540His",
"transcript": "XM_017005266.3",
"protein_id": "XP_016860755.1",
"transcript_support_level": null,
"aa_start": 540,
"aa_end": null,
"aa_length": 665,
"cds_start": 1619,
"cds_end": null,
"cds_length": 1998,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017005266.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "n.320G>A",
"hgvs_p": null,
"transcript": "ENST00000450650.5",
"protein_id": "ENSP00000403180.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000450650.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "n.1808G>A",
"hgvs_p": null,
"transcript": "XR_939741.4",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_939741.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"hgvs_c": "n.1808G>A",
"hgvs_p": null,
"transcript": "XR_939742.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_939742.3"
}
],
"gene_symbol": "CAPN13",
"gene_hgnc_id": 16663,
"dbsnp": "rs745335171",
"frequency_reference_population": 0.0000074361697,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000752556,
"gnomad_genomes_af": 0.00000657687,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5299063324928284,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.12999999523162842,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.172,
"revel_prediction": "Benign",
"alphamissense_score": 0.1674,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.229,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.13,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_144575.3",
"gene_symbol": "CAPN13",
"hgnc_id": 16663,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Arg544His"
}
],
"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
}