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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: 12-21604477-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=21604477&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 21604477,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_021957.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "NM_021957.4",
"protein_id": "NP_068776.2",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 703,
"cds_start": 116,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 371,
"cdna_end": null,
"cdna_length": 3214,
"mane_select": "ENST00000261195.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021957.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "ENST00000261195.3",
"protein_id": "ENSP00000261195.2",
"transcript_support_level": 1,
"aa_start": 39,
"aa_end": null,
"aa_length": 703,
"cds_start": 116,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 371,
"cdna_end": null,
"cdna_length": 3214,
"mane_select": "NM_021957.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261195.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285854",
"gene_hgnc_id": null,
"hgvs_c": "n.*124-23954A>G",
"hgvs_p": null,
"transcript": "ENST00000647960.1",
"protein_id": "ENSP00000497202.1",
"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": 3765,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000647960.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "ENST00000863011.1",
"protein_id": "ENSP00000533070.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 741,
"cds_start": 116,
"cds_end": null,
"cds_length": 2226,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 3315,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863011.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "ENST00000863012.1",
"protein_id": "ENSP00000533071.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 732,
"cds_start": 116,
"cds_end": null,
"cds_length": 2199,
"cdna_start": 390,
"cdna_end": null,
"cdna_length": 3237,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863012.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "ENST00000863013.1",
"protein_id": "ENSP00000533072.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 686,
"cds_start": 116,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 384,
"cdna_end": null,
"cdna_length": 3084,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863013.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "ENST00000863014.1",
"protein_id": "ENSP00000533073.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 676,
"cds_start": 116,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 371,
"cdna_end": null,
"cdna_length": 3049,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863014.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "ENST00000863010.1",
"protein_id": "ENSP00000533069.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 671,
"cds_start": 116,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 3142,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863010.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "ENST00000863015.1",
"protein_id": "ENSP00000533074.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 665,
"cds_start": 116,
"cds_end": null,
"cds_length": 1998,
"cdna_start": 158,
"cdna_end": null,
"cdna_length": 2133,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000863015.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "XM_024448960.2",
"protein_id": "XP_024304728.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 703,
"cds_start": 116,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 371,
"cdna_end": null,
"cdna_length": 3119,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024448960.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser",
"transcript": "XM_017019245.3",
"protein_id": "XP_016874734.1",
"transcript_support_level": null,
"aa_start": 39,
"aa_end": null,
"aa_length": 392,
"cds_start": 116,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 371,
"cdna_end": null,
"cdna_length": 1893,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017019245.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285854",
"gene_hgnc_id": null,
"hgvs_c": "n.107-23954A>G",
"hgvs_p": null,
"transcript": "ENST00000648372.1",
"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": 2635,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000648372.1"
}
],
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"dbsnp": "rs121918423",
"frequency_reference_population": 0.00005118397,
"hom_count_reference_population": 0,
"allele_count_reference_population": 82,
"gnomad_exomes_af": 0.0000510367,
"gnomad_genomes_af": 0.000052588,
"gnomad_exomes_ac": 74,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9440497159957886,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.571,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3424,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.181,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PS3",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_021957.4",
"gene_symbol": "GYS2",
"hgnc_id": 4707,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asn39Ser"
},
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PS3",
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000647960.1",
"gene_symbol": "ENSG00000285854",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*124-23954A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Glycogen storage disorder due to hepatic glycogen synthase deficiency",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"phenotype_combined": "Glycogen storage disorder due to hepatic glycogen synthase deficiency",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}