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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: 11-65206551-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=65206551&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CAPN1",
"hgnc_id": 1476,
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_005186.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 5,
"alphamissense_prediction": null,
"alphamissense_score": 0.9942,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Autosomal recessive spastic paraplegia type 76",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9460494518280029,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2952,
"cdna_start": 1529,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_005186.4",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000279247.11",
"protein_coding": true,
"protein_id": "NP_005177.2",
"strand": true,
"transcript": "NM_005186.4",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2952,
"cdna_start": 1529,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000279247.11",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005186.4",
"protein_coding": true,
"protein_id": "ENSP00000279247.7",
"strand": true,
"transcript": "ENST00000279247.11",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2960,
"cdna_start": 1542,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000524773.5",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000434176.1",
"strand": true,
"transcript": "ENST00000524773.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3086,
"cdna_start": 1682,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000527323.5",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000431984.1",
"strand": true,
"transcript": "ENST00000527323.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3083,
"cdna_start": 1660,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000533820.5",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000435272.1",
"strand": true,
"transcript": "ENST00000533820.5",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2904,
"cdna_start": 1481,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001198868.2",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001185797.1",
"strand": true,
"transcript": "NM_001198868.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2916,
"cdna_start": 1493,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001198869.2",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001185798.1",
"strand": true,
"transcript": "NM_001198869.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2792,
"cdna_start": 1517,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000533129.5",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000431686.1",
"strand": true,
"transcript": "ENST00000533129.5",
"transcript_support_level": 5
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3276,
"cdna_start": 1853,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_006718698.3",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006718761.1",
"strand": true,
"transcript": "XM_006718698.3",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 481,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2956,
"cdna_start": 1533,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1442,
"consequences": [
"missense_variant"
],
"exon_count": 22,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_011545292.2",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1442G>A",
"hgvs_p": "p.Arg481Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011543594.1",
"strand": true,
"transcript": "XM_011545292.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 626,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2679,
"cdna_start": null,
"cds_end": null,
"cds_length": 1881,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000903824.1",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "c.1342-1504G>A",
"hgvs_p": null,
"intron_rank": 11,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000573883.1",
"strand": true,
"transcript": "ENST00000903824.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 643,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000525013.1",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "n.295G>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": "ENST00000525013.1",
"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": 572,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000530495.1",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "n.454G>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": "ENST00000530495.1",
"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": 2882,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NR_040008.2",
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"hgvs_c": "n.1459G>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": "NR_040008.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs763471308",
"effect": "missense_variant",
"frequency_reference_population": 0.0000030991646,
"gene_hgnc_id": 1476,
"gene_symbol": "CAPN1",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000136881,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197083,
"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": "Uncertain significance",
"phenotype_combined": "Autosomal recessive spastic paraplegia type 76",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.889,
"pos": 65206551,
"ref": "G",
"revel_prediction": "Pathogenic",
"revel_score": 0.911,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05999999865889549,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.06,
"transcript": "NM_005186.4"
}
]
}