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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-21977174-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=21977174&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 21977174,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000404933.7",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "c.443A>G",
"hgvs_p": "p.Gln148Arg",
"transcript": "NM_004595.5",
"protein_id": "NP_004586.2",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 366,
"cds_start": 443,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 559,
"cdna_end": null,
"cdna_length": 1703,
"mane_select": "ENST00000404933.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "c.443A>G",
"hgvs_p": "p.Gln148Arg",
"transcript": "ENST00000404933.7",
"protein_id": "ENSP00000385746.2",
"transcript_support_level": 1,
"aa_start": 148,
"aa_end": null,
"aa_length": 366,
"cds_start": 443,
"cds_end": null,
"cds_length": 1101,
"cdna_start": 559,
"cdna_end": null,
"cdna_length": 1703,
"mane_select": "NM_004595.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "c.788A>G",
"hgvs_p": "p.Gln263Arg",
"transcript": "ENST00000457085.2",
"protein_id": "ENSP00000407366.2",
"transcript_support_level": 5,
"aa_start": 263,
"aa_end": null,
"aa_length": 333,
"cds_start": 788,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 821,
"cdna_end": null,
"cdna_length": 1035,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "c.284A>G",
"hgvs_p": "p.Gln95Arg",
"transcript": "NM_001258423.2",
"protein_id": "NP_001245352.1",
"transcript_support_level": null,
"aa_start": 95,
"aa_end": null,
"aa_length": 313,
"cds_start": 284,
"cds_end": null,
"cds_length": 942,
"cdna_start": 400,
"cdna_end": null,
"cdna_length": 1544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "c.284A>G",
"hgvs_p": "p.Gln95Arg",
"transcript": "ENST00000379404.5",
"protein_id": "ENSP00000368714.1",
"transcript_support_level": 3,
"aa_start": 95,
"aa_end": null,
"aa_length": 313,
"cds_start": 284,
"cds_end": null,
"cds_length": 942,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 1174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.Gln114Arg",
"transcript": "XM_005274582.3",
"protein_id": "XP_005274639.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 332,
"cds_start": 341,
"cds_end": null,
"cds_length": 999,
"cdna_start": 528,
"cdna_end": null,
"cdna_length": 1672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "c.341A>G",
"hgvs_p": "p.Gln114Arg",
"transcript": "XM_011545568.3",
"protein_id": "XP_011543870.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 332,
"cds_start": 341,
"cds_end": null,
"cds_length": 999,
"cdna_start": 765,
"cdna_end": null,
"cdna_length": 1909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"hgvs_c": "n.396A>G",
"hgvs_p": null,
"transcript": "ENST00000478094.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMS",
"gene_hgnc_id": 11123,
"dbsnp": "rs397515551",
"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": 0.9888377785682678,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.877,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9855,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.904,
"phylop100way_prediction": "Pathogenic",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000404933.7",
"gene_symbol": "SMS",
"hgnc_id": 11123,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.443A>G",
"hgvs_p": "p.Gln148Arg"
}
],
"clinvar_disease": "Syndromic X-linked intellectual disability Snyder type",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Syndromic X-linked intellectual disability Snyder type",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}