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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: 3-50341486-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=50341486&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 50341486,
"ref": "C",
"alt": "A",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "NM_015896.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"hgvs_c": "c.1248-1G>T",
"hgvs_p": null,
"transcript": "NM_015896.4",
"protein_id": "NP_056980.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 440,
"cds_start": -4,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": "ENST00000231749.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"hgvs_c": "c.1248-1G>T",
"hgvs_p": null,
"transcript": "ENST00000231749.8",
"protein_id": "ENSP00000231749.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 440,
"cds_start": -4,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": "NM_015896.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"hgvs_c": "c.1233-1G>T",
"hgvs_p": null,
"transcript": "ENST00000360165.7",
"protein_id": "ENSP00000353289.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 435,
"cds_start": -4,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1757,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"hgvs_c": "c.1233-1G>T",
"hgvs_p": null,
"transcript": "NM_001308379.2",
"protein_id": "NP_001295308.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 435,
"cds_start": -4,
"cds_end": null,
"cds_length": 1308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1759,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ZMYND10-AS1",
"gene_hgnc_id": 40890,
"hgvs_c": "n.123+258C>A",
"hgvs_p": null,
"transcript": "ENST00000440013.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"hgvs_c": "n.1403-1G>T",
"hgvs_p": null,
"transcript": "ENST00000475688.1",
"protein_id": null,
"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": 1773,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"hgvs_c": "n.301-1G>T",
"hgvs_p": null,
"transcript": "ENST00000490675.5",
"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": 676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"hgvs_c": "c.1011-1G>T",
"hgvs_p": null,
"transcript": "XM_005265216.4",
"protein_id": "XP_005265273.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 361,
"cds_start": -4,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZMYND10",
"gene_hgnc_id": 19412,
"dbsnp": "rs145320643",
"frequency_reference_population": 0.000015488316,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000157332,
"gnomad_genomes_af": 0.000013137,
"gnomad_exomes_ac": 23,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1599999964237213,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.949999988079071,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.062,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.91,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999971209564868,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_015896.4",
"gene_symbol": "ZMYND10",
"hgnc_id": 19412,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1248-1G>T",
"hgvs_p": null
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000440013.1",
"gene_symbol": "ZMYND10-AS1",
"hgnc_id": 40890,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.123+258C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Primary ciliary dyskinesia 22",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Primary ciliary dyskinesia 22",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}