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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: X-101412604-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=101412604&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 101412604,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000316594.6",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HNRNPH2",
"gene_hgnc_id": 5042,
"hgvs_c": "c.616C>T",
"hgvs_p": "p.Arg206Trp",
"transcript": "NM_019597.5",
"protein_id": "NP_062543.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 449,
"cds_start": 616,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 2296,
"mane_select": "ENST00000316594.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HNRNPH2",
"gene_hgnc_id": 5042,
"hgvs_c": "c.616C>T",
"hgvs_p": "p.Arg206Trp",
"transcript": "ENST00000316594.6",
"protein_id": "ENSP00000361927.2",
"transcript_support_level": 1,
"aa_start": 206,
"aa_end": null,
"aa_length": 449,
"cds_start": 616,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 2296,
"mane_select": "NM_019597.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HNRNPH2",
"gene_hgnc_id": 5042,
"hgvs_c": "c.616C>T",
"hgvs_p": "p.Arg206Trp",
"transcript": "NM_001032393.3",
"protein_id": "NP_001027565.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 449,
"cds_start": 616,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 755,
"cdna_end": null,
"cdna_length": 2284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL36A-HNRNPH2",
"gene_hgnc_id": 48349,
"hgvs_c": "c.*612C>T",
"hgvs_p": null,
"transcript": "NM_001199973.2",
"protein_id": "NP_001186902.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 118,
"cds_start": -4,
"cds_end": null,
"cds_length": 357,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPL36A-HNRNPH2",
"gene_hgnc_id": 48349,
"hgvs_c": "c.*612C>T",
"hgvs_p": null,
"transcript": "NM_001199974.2",
"protein_id": "NP_001186903.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 77,
"cds_start": -4,
"cds_end": null,
"cds_length": 234,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HNRNPH2",
"gene_hgnc_id": 5042,
"dbsnp": "rs886039763",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.583834171295166,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.185,
"revel_prediction": "Benign",
"alphamissense_score": 0.974,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.27,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.627,
"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": 15,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 15,
"benign_score": 0,
"pathogenic_score": 15,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000316594.6",
"gene_symbol": "HNRNPH2",
"hgnc_id": 5042,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.616C>T",
"hgvs_p": "p.Arg206Trp"
},
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_001199973.2",
"gene_symbol": "RPL36A-HNRNPH2",
"hgnc_id": 48349,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*612C>T",
"hgvs_p": null
}
],
"clinvar_disease": " Bain type, X-linked, syndromic,Abnormal facial shape,Inborn genetic diseases,Intellectual disability,Neurodevelopmental delay,Neurodevelopmental disorder,Stereotypic movement disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:24 LP:1",
"phenotype_combined": "Intellectual disability, X-linked, syndromic, Bain type|not provided|Inborn genetic diseases|Neurodevelopmental disorder|Stereotypic movement disorder;Abnormal facial shape|Neurodevelopmental delay",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}