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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: 3-81642787-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=81642787&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 81642787,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000158.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.986A>C",
"hgvs_p": "p.Tyr329Ser",
"transcript": "NM_000158.4",
"protein_id": "NP_000149.4",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 702,
"cds_start": 986,
"cds_end": null,
"cds_length": 2109,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000429644.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000158.4"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.986A>C",
"hgvs_p": "p.Tyr329Ser",
"transcript": "ENST00000429644.7",
"protein_id": "ENSP00000410833.2",
"transcript_support_level": 1,
"aa_start": 329,
"aa_end": null,
"aa_length": 702,
"cds_start": 986,
"cds_end": null,
"cds_length": 2109,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000158.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000429644.7"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.986A>C",
"hgvs_p": "p.Tyr329Ser",
"transcript": "ENST00000895874.1",
"protein_id": "ENSP00000565933.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 700,
"cds_start": 986,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000895874.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.980A>C",
"hgvs_p": "p.Tyr327Ser",
"transcript": "ENST00000942742.1",
"protein_id": "ENSP00000612801.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 700,
"cds_start": 980,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942742.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.986A>C",
"hgvs_p": "p.Tyr329Ser",
"transcript": "ENST00000942738.1",
"protein_id": "ENSP00000612797.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 669,
"cds_start": 986,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942738.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.863A>C",
"hgvs_p": "p.Tyr288Ser",
"transcript": "ENST00000489715.1",
"protein_id": "ENSP00000419638.1",
"transcript_support_level": 2,
"aa_start": 288,
"aa_end": null,
"aa_length": 661,
"cds_start": 863,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000489715.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.986A>C",
"hgvs_p": "p.Tyr329Ser",
"transcript": "ENST00000942741.1",
"protein_id": "ENSP00000612800.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 619,
"cds_start": 986,
"cds_end": null,
"cds_length": 1860,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942741.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.986A>C",
"hgvs_p": "p.Tyr329Ser",
"transcript": "ENST00000942739.1",
"protein_id": "ENSP00000612798.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 532,
"cds_start": 986,
"cds_end": null,
"cds_length": 1599,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942739.1"
},
{
"aa_ref": "Y",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.347A>C",
"hgvs_p": "p.Tyr116Ser",
"transcript": "ENST00000942740.1",
"protein_id": "ENSP00000612799.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 489,
"cds_start": 347,
"cds_end": null,
"cds_length": 1470,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942740.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "c.782+3605A>C",
"hgvs_p": null,
"transcript": "ENST00000895875.1",
"protein_id": "ENSP00000565934.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 632,
"cds_start": null,
"cds_end": null,
"cds_length": 1899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000895875.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "n.536A>C",
"hgvs_p": null,
"transcript": "ENST00000498468.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000498468.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"hgvs_c": "n.1114A>C",
"hgvs_p": null,
"transcript": "XR_007095662.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007095662.1"
}
],
"gene_symbol": "GBE1",
"gene_hgnc_id": 4180,
"dbsnp": "rs80338671",
"frequency_reference_population": 0.00017216618,
"hom_count_reference_population": 0,
"allele_count_reference_population": 275,
"gnomad_exomes_af": 0.000170206,
"gnomad_genomes_af": 0.000190802,
"gnomad_exomes_ac": 246,
"gnomad_genomes_ac": 29,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.28169453144073486,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.946,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8395,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.554,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PM5,PP3,PP5_Very_Strong,BP4",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 1,
"pathogenic_score": 17,
"criteria": [
"PS3",
"PM2",
"PM5",
"PP3",
"PP5_Very_Strong",
"BP4"
],
"verdict": "Pathogenic",
"transcript": "NM_000158.4",
"gene_symbol": "GBE1",
"hgnc_id": 4180,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.986A>C",
"hgvs_p": "p.Tyr329Ser"
}
],
"clinvar_disease": " classic hepatic, nonprogressive hepatic, type IV,Adult polyglucosan body disease,Adult polyglucosan body neuropathy,GBE1-related disorder,Glycogen storage disease,Glycogen storage disease IV,Inborn genetic diseases,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:17 O:1",
"phenotype_combined": "Glycogen storage disease IV, nonprogressive hepatic|Glycogen storage disease, type IV|GBE1-related disorder|Glycogen storage disease IV, classic hepatic;Glycogen storage disease, type IV|Adult polyglucosan body neuropathy|Adult polyglucosan body disease;Glycogen storage disease, type IV|not provided|Adult polyglucosan body disease|Inborn genetic diseases",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}