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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: 3-149026841-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=149026841&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 149026841,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000345003.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.961C>T",
"hgvs_p": "p.Arg321Trp",
"transcript": "NM_004130.4",
"protein_id": "NP_004121.2",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 350,
"cds_start": 961,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 5996,
"mane_select": "ENST00000345003.9",
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.961C>T",
"hgvs_p": "p.Arg321Trp",
"transcript": "ENST00000345003.9",
"protein_id": "ENSP00000340736.4",
"transcript_support_level": 1,
"aa_start": 321,
"aa_end": null,
"aa_length": 350,
"cds_start": 961,
"cds_end": null,
"cds_length": 1053,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 5996,
"mane_select": "NM_004130.4",
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.910C>T",
"hgvs_p": "p.Arg304Trp",
"transcript": "ENST00000296048.10",
"protein_id": "ENSP00000296048.6",
"transcript_support_level": 1,
"aa_start": 304,
"aa_end": null,
"aa_length": 333,
"cds_start": 910,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 1099,
"cdna_end": null,
"cdna_length": 1890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.690C>T",
"hgvs_p": "p.Asn230Asn",
"transcript": "ENST00000484197.5",
"protein_id": "ENSP00000420683.1",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 279,
"cds_start": 690,
"cds_end": null,
"cds_length": 840,
"cdna_start": 773,
"cdna_end": null,
"cdna_length": 1563,
"mane_select": null,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.910C>T",
"hgvs_p": "p.Arg304Trp",
"transcript": "NM_001184720.2",
"protein_id": "NP_001171649.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 333,
"cds_start": 910,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 1011,
"cdna_end": null,
"cdna_length": 5945,
"mane_select": null,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.733C>T",
"hgvs_p": "p.Arg245Trp",
"transcript": "XM_017006275.2",
"protein_id": "XP_016861764.1",
"transcript_support_level": null,
"aa_start": 245,
"aa_end": null,
"aa_length": 274,
"cds_start": 733,
"cds_end": null,
"cds_length": 825,
"cdna_start": 875,
"cdna_end": null,
"cdna_length": 5809,
"mane_select": null,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.448C>T",
"hgvs_p": "p.Arg150Trp",
"transcript": "XM_017006276.2",
"protein_id": "XP_016861765.1",
"transcript_support_level": null,
"aa_start": 150,
"aa_end": null,
"aa_length": 179,
"cds_start": 448,
"cds_end": null,
"cds_length": 540,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 6356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.690C>T",
"hgvs_p": "p.Asn230Asn",
"transcript": "NM_001184721.2",
"protein_id": "NP_001171650.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 279,
"cds_start": 690,
"cds_end": null,
"cds_length": 840,
"cdna_start": 791,
"cdna_end": null,
"cdna_length": 5725,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "n.306C>T",
"hgvs_p": null,
"transcript": "ENST00000479119.1",
"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": 812,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"hgvs_c": "c.*189C>T",
"hgvs_p": null,
"transcript": "ENST00000627418.2",
"protein_id": "ENSP00000486061.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": -4,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1831,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GYG1",
"gene_hgnc_id": 4699,
"dbsnp": "rs138596591",
"frequency_reference_population": 0.000032840195,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000232617,
"gnomad_genomes_af": 0.0001248,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 19,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.621953010559082,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.646,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5451,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.964,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000345003.9",
"gene_symbol": "GYG1",
"hgnc_id": 4699,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.961C>T",
"hgvs_p": "p.Arg321Trp"
}
],
"clinvar_disease": "Glycogen storage disease XV,Inborn genetic diseases,Polyglucosan body myopathy type 2",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Glycogen storage disease XV;Polyglucosan body myopathy type 2|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}