← Back to variant description
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: 1-225921590-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=225921590&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 225921590,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000343818.11",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "c.595C>T",
"hgvs_p": "p.Arg199Trp",
"transcript": "NM_013328.4",
"protein_id": "NP_037460.2",
"transcript_support_level": null,
"aa_start": 199,
"aa_end": null,
"aa_length": 320,
"cds_start": 595,
"cds_end": null,
"cds_length": 963,
"cdna_start": 735,
"cdna_end": null,
"cdna_length": 1680,
"mane_select": "ENST00000343818.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "c.595C>T",
"hgvs_p": "p.Arg199Trp",
"transcript": "ENST00000343818.11",
"protein_id": "ENSP00000342502.6",
"transcript_support_level": 1,
"aa_start": 199,
"aa_end": null,
"aa_length": 320,
"cds_start": 595,
"cds_end": null,
"cds_length": 963,
"cdna_start": 735,
"cdna_end": null,
"cdna_length": 1680,
"mane_select": "NM_013328.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255835",
"gene_hgnc_id": null,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Arg125Trp",
"transcript": "ENST00000432920.2",
"protein_id": "ENSP00000414068.2",
"transcript_support_level": 2,
"aa_start": 125,
"aa_end": null,
"aa_length": 359,
"cds_start": 373,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 541,
"cdna_end": null,
"cdna_length": 1625,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Arg125Trp",
"transcript": "NM_001271681.2",
"protein_id": "NP_001258610.1",
"transcript_support_level": null,
"aa_start": 125,
"aa_end": null,
"aa_length": 246,
"cds_start": 373,
"cds_end": null,
"cds_length": 741,
"cdna_start": 513,
"cdna_end": null,
"cdna_length": 1458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Arg125Trp",
"transcript": "ENST00000612039.4",
"protein_id": "ENSP00000478165.1",
"transcript_support_level": 3,
"aa_start": 125,
"aa_end": null,
"aa_length": 246,
"cds_start": 373,
"cds_end": null,
"cds_length": 741,
"cdna_start": 603,
"cdna_end": null,
"cdna_length": 1549,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "n.1153C>T",
"hgvs_p": null,
"transcript": "ENST00000446534.1",
"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": 1341,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "n.132C>T",
"hgvs_p": null,
"transcript": "ENST00000466127.1",
"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": 506,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "n.2204C>T",
"hgvs_p": null,
"transcript": "ENST00000478402.5",
"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": 3149,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"hgvs_c": "c.*14C>T",
"hgvs_p": null,
"transcript": "ENST00000489681.5",
"protein_id": "ENSP00000482614.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 156,
"cds_start": -4,
"cds_end": null,
"cds_length": 473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PYCR2",
"gene_hgnc_id": 30262,
"dbsnp": "rs758595075",
"frequency_reference_population": 0.000013630106,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000136809,
"gnomad_genomes_af": 0.000013142,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8598552942276001,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.739,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.674,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.699,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.18,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000343818.11",
"gene_symbol": "PYCR2",
"hgnc_id": 30262,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.595C>T",
"hgvs_p": "p.Arg199Trp"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000432920.2",
"gene_symbol": "ENSG00000255835",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.373C>T",
"hgvs_p": "p.Arg125Trp"
}
],
"clinvar_disease": "Hypomyelinating leukodystrophy 10,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 US:1",
"phenotype_combined": "Hypomyelinating leukodystrophy 10|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}