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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: 12-21536548-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=21536548&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "GYS2",
"hgnc_id": 4707,
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "NM_021957.4",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000285854",
"hgnc_id": null,
"hgvs_c": "n.*2520T>G",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000647960.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "SPX",
"hgnc_id": 28139,
"hgvs_c": "n.472-498A>C",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -4,
"transcript": "ENST00000537527.1",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC124902896",
"hgnc_id": null,
"hgvs_c": "n.519-498A>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "XR_007063240.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_score": -4,
"allele_count_reference_population": 12,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.83,
"chr": "12",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Glycogen storage disorder due to hepatic glycogen synthase deficiency",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8299999833106995,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 703,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3214,
"cdna_start": null,
"cds_end": null,
"cds_length": 2112,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_021957.4",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": null,
"aa_end": null,
"aa_length": 703,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3214,
"cdna_start": null,
"cds_end": null,
"cds_length": 2112,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000261195.3",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": 23,
"exon_rank_end": null,
"feature": "ENST00000647960.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285854",
"hgvs_c": "n.*2520T>G",
"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": 23,
"exon_rank_end": null,
"feature": "ENST00000647960.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000285854",
"hgvs_c": "n.*2520T>G",
"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": 741,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3315,
"cdna_start": null,
"cds_end": null,
"cds_length": 2226,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000863011.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": null,
"aa_end": null,
"aa_length": 732,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3237,
"cdna_start": null,
"cds_end": null,
"cds_length": 2199,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000863012.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": null,
"aa_end": null,
"aa_length": 686,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3084,
"cdna_start": null,
"cds_end": null,
"cds_length": 2061,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 16,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000863013.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": null,
"aa_end": null,
"aa_length": 676,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3049,
"cdna_start": null,
"cds_end": null,
"cds_length": 2031,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000863014.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": null,
"aa_end": null,
"aa_length": 671,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3142,
"cdna_start": null,
"cds_end": null,
"cds_length": 2016,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000863010.1",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": null,
"aa_end": null,
"aa_length": 626,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2745,
"cdna_start": null,
"cds_end": null,
"cds_length": 1881,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 15,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_006719063.4",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*406T>G",
"hgvs_p": null,
"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": 703,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3119,
"cdna_start": null,
"cds_end": null,
"cds_length": 2112,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 17,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024448960.2",
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"hgvs_c": "c.*42+364T>G",
"hgvs_p": null,
"intron_rank": 16,
"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": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 803,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000537527.1",
"gene_hgnc_id": 28139,
"gene_symbol": "SPX",
"hgvs_c": "n.472-498A>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000537527.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4732,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000649016.1",
"gene_hgnc_id": 28139,
"gene_symbol": "SPX",
"hgvs_c": "n.529-498A>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000649016.1",
"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": 806,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007063240.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124902896",
"hgvs_c": "n.519-498A>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007063240.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs886445298",
"effect": "3_prime_UTR_variant",
"frequency_reference_population": 0.00005196425,
"gene_hgnc_id": 4707,
"gene_symbol": "GYS2",
"gnomad_exomes_ac": 6,
"gnomad_exomes_af": 0.0000762098,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 6,
"gnomad_genomes_af": 0.0000394223,
"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": "Uncertain significance",
"phenotype_combined": "Glycogen storage disorder due to hepatic glycogen synthase deficiency",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.785,
"pos": 21536548,
"ref": "A",
"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"
}
]
}