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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: 11-74253493-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=74253493&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 74253493,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_016147.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Val382Met",
"transcript": "NM_016147.3",
"protein_id": "NP_057231.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 386,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 1277,
"cdna_end": null,
"cdna_length": 2487,
"mane_select": "ENST00000328257.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Val382Met",
"transcript": "ENST00000328257.13",
"protein_id": "ENSP00000329867.8",
"transcript_support_level": 1,
"aa_start": 382,
"aa_end": null,
"aa_length": 386,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 1277,
"cdna_end": null,
"cdna_length": 2487,
"mane_select": "NM_016147.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "c.1186G>A",
"hgvs_p": "p.Val396Met",
"transcript": "ENST00000398427.6",
"protein_id": "ENSP00000381461.4",
"transcript_support_level": 1,
"aa_start": 396,
"aa_end": null,
"aa_length": 400,
"cds_start": 1186,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 1286,
"cdna_end": null,
"cdna_length": 2496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "n.674G>A",
"hgvs_p": null,
"transcript": "ENST00000538501.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 744,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "n.2408G>A",
"hgvs_p": null,
"transcript": "ENST00000541340.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "n.718G>A",
"hgvs_p": null,
"transcript": "ENST00000543525.3",
"protein_id": null,
"transcript_support_level": 1,
"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": 1928,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "P4HA3",
"gene_hgnc_id": 30135,
"hgvs_c": "n.*1319-5492C>T",
"hgvs_p": null,
"transcript": "ENST00000524388.5",
"protein_id": "ENSP00000433860.1",
"transcript_support_level": 1,
"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": 2627,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "c.1186G>A",
"hgvs_p": "p.Val396Met",
"transcript": "NM_001271593.2",
"protein_id": "NP_001258522.1",
"transcript_support_level": null,
"aa_start": 396,
"aa_end": null,
"aa_length": 400,
"cds_start": 1186,
"cds_end": null,
"cds_length": 1203,
"cdna_start": 1319,
"cdna_end": null,
"cdna_length": 2529,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"hgvs_c": "n.2846G>A",
"hgvs_p": null,
"transcript": "ENST00000539021.1",
"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": 4055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "P4HA3",
"gene_hgnc_id": 30135,
"hgvs_c": "n.1946-3171C>T",
"hgvs_p": null,
"transcript": "XR_007062475.1",
"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": 2122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PPME1",
"gene_hgnc_id": 30178,
"dbsnp": "rs200531037",
"frequency_reference_population": 0.000016794951,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.00000755756,
"gnomad_genomes_af": 0.000105173,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15410718321800232,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.041999999433755875,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.225,
"revel_prediction": "Benign",
"alphamissense_score": 0.2446,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.482,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0010046877664449,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_016147.3",
"gene_symbol": "PPME1",
"hgnc_id": 30178,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Val382Met"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000524388.5",
"gene_symbol": "P4HA3",
"hgnc_id": 30135,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*1319-5492C>T",
"hgvs_p": null
}
],
"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
}