← Back to variant description
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: 12-21559148-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=21559148&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "GYS2",
"hgnc_id": 4707,
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_021957.4",
"verdict": "Likely_benign"
},
{
"benign_score": 3,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000285854",
"hgnc_id": null,
"hgvs_c": "n.*1253C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -1,
"transcript": "ENST00000647960.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6,BP7",
"acmg_score": -2,
"allele_count_reference_population": 372,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.41,
"chr": "12",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Glycogen storage disorder due to hepatic glycogen synthase deficiency,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.4099999964237213,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 703,
"aa_ref": "N",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3214,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 2112,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_021957.4",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261195.3",
"protein_coding": true,
"protein_id": "NP_068776.2",
"strand": false,
"transcript": "NM_021957.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 703,
"aa_ref": "N",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3214,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 2112,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000261195.3",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021957.4",
"protein_coding": true,
"protein_id": "ENSP00000261195.2",
"strand": false,
"transcript": "ENST00000261195.3",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 3765,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000647960.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285854",
"hgvs_c": "n.*1253C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000497202.1",
"strand": false,
"transcript": "ENST00000647960.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 3765,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 23,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000647960.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285854",
"hgvs_c": "n.*1253C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000497202.1",
"strand": false,
"transcript": "ENST00000647960.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 741,
"aa_ref": "N",
"aa_start": 455,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3315,
"cdna_start": 1690,
"cds_end": null,
"cds_length": 2226,
"cds_start": 1365,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000863011.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1365C>T",
"hgvs_p": "p.Asn455Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533070.1",
"strand": false,
"transcript": "ENST00000863011.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 732,
"aa_ref": "N",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3237,
"cdna_start": 1525,
"cds_end": null,
"cds_length": 2199,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000863012.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533071.1",
"strand": false,
"transcript": "ENST00000863012.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 686,
"aa_ref": "N",
"aa_start": 400,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3084,
"cdna_start": 1468,
"cds_end": null,
"cds_length": 2061,
"cds_start": 1200,
"consequences": [
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000863013.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1200C>T",
"hgvs_p": "p.Asn400Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533072.1",
"strand": false,
"transcript": "ENST00000863013.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 676,
"aa_ref": "N",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3049,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 2031,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000863014.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533073.1",
"strand": false,
"transcript": "ENST00000863014.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 671,
"aa_ref": "N",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3142,
"cdna_start": 1538,
"cds_end": null,
"cds_length": 2016,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000863010.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533069.1",
"strand": false,
"transcript": "ENST00000863010.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 665,
"aa_ref": "N",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2133,
"cdna_start": 1293,
"cds_end": null,
"cds_length": 1998,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000863015.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000533074.1",
"strand": false,
"transcript": "ENST00000863015.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 703,
"aa_ref": "N",
"aa_start": 417,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3119,
"cdna_start": 1506,
"cds_end": null,
"cds_length": 2112,
"cds_start": 1251,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_024448960.2",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1251C>T",
"hgvs_p": "p.Asn417Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024304728.1",
"strand": false,
"transcript": "XM_024448960.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 626,
"aa_ref": "N",
"aa_start": 340,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2745,
"cdna_start": 1037,
"cds_end": null,
"cds_length": 1881,
"cds_start": 1020,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_006719063.4",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.1020C>T",
"hgvs_p": "p.Asn340Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006719126.1",
"strand": false,
"transcript": "XM_006719063.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2635,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000648372.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285854",
"hgvs_c": "n.1178C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000648372.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs139882761",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00023154344,
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"gnomad_exomes_ac": 326,
"gnomad_exomes_af": 0.000224089,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 46,
"gnomad_genomes_af": 0.000302974,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Glycogen storage disorder due to hepatic glycogen synthase deficiency|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.067,
"pos": 21559148,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_021957.4"
}
]
}