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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: 7-16406249-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=16406249&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 16406249,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000407010.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Cys",
"transcript": "NM_001101426.4",
"protein_id": "NP_001094896.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 451,
"cds_start": 346,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 5742,
"mane_select": "ENST00000407010.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Cys",
"transcript": "ENST00000407010.7",
"protein_id": "ENSP00000385478.2",
"transcript_support_level": 5,
"aa_start": 116,
"aa_end": null,
"aa_length": 451,
"cds_start": 346,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 5742,
"mane_select": "NM_001101426.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Cys",
"transcript": "ENST00000399310.3",
"protein_id": "ENSP00000382249.3",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 401,
"cds_start": 346,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 346,
"cdna_end": null,
"cdna_length": 1709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Cys",
"transcript": "NM_001368197.1",
"protein_id": "NP_001355126.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 416,
"cds_start": 346,
"cds_end": null,
"cds_length": 1251,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 5637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Cys",
"transcript": "NM_001101417.4",
"protein_id": "NP_001094887.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 401,
"cds_start": 346,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 562,
"cdna_end": null,
"cdna_length": 5592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.43C>T",
"hgvs_p": "p.Arg15Cys",
"transcript": "ENST00000676325.1",
"protein_id": "ENSP00000502074.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 350,
"cds_start": 43,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 2008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.43C>T",
"hgvs_p": "p.Arg15Cys",
"transcript": "ENST00000675257.1",
"protein_id": "ENSP00000501664.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 315,
"cds_start": 43,
"cds_end": null,
"cds_length": 948,
"cdna_start": 311,
"cdna_end": null,
"cdna_length": 1415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.43C>T",
"hgvs_p": "p.Arg15Cys",
"transcript": "ENST00000674759.1",
"protein_id": "ENSP00000502749.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 300,
"cds_start": 43,
"cds_end": null,
"cds_length": 903,
"cdna_start": 321,
"cdna_end": null,
"cdna_length": 1181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "n.562C>T",
"hgvs_p": null,
"transcript": "NR_160656.1",
"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": 5591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"dbsnp": "rs61744487",
"frequency_reference_population": 0.000989542,
"hom_count_reference_population": 16,
"allele_count_reference_population": 1597,
"gnomad_exomes_af": 0.000550072,
"gnomad_genomes_af": 0.00520847,
"gnomad_exomes_ac": 804,
"gnomad_genomes_ac": 793,
"gnomad_exomes_homalt": 11,
"gnomad_genomes_homalt": 5,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.012536793947219849,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.32,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1023,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.625,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000407010.7",
"gene_symbol": "CRPPA",
"hgnc_id": 37276,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.346C>T",
"hgvs_p": "p.Arg116Cys"
}
],
"clinvar_disease": " 7, alpha-dystroglycan related, type A,Autosomal recessive limb-girdle muscular dystrophy type 2U,Congenital Muscular Dystrophy,Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies),not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:2",
"phenotype_combined": "Congenital Muscular Dystrophy, alpha-dystroglycan related|not specified|Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7;Autosomal recessive limb-girdle muscular dystrophy type 2U|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}