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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: 12-21562965-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=21562965&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 21562965,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000261195.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "P",
"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": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.1015G>C",
"hgvs_p": "p.Ala339Pro",
"transcript": "NM_021957.4",
"protein_id": "NP_068776.2",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 703,
"cds_start": 1015,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 3214,
"mane_select": "ENST00000261195.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"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": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.1015G>C",
"hgvs_p": "p.Ala339Pro",
"transcript": "ENST00000261195.3",
"protein_id": "ENSP00000261195.2",
"transcript_support_level": 1,
"aa_start": 339,
"aa_end": null,
"aa_length": 703,
"cds_start": 1015,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 3214,
"mane_select": "NM_021957.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285854",
"gene_hgnc_id": null,
"hgvs_c": "n.*1017G>C",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285854",
"gene_hgnc_id": null,
"hgvs_c": "n.*1017G>C",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.1015G>C",
"hgvs_p": "p.Ala339Pro",
"transcript": "XM_024448960.2",
"protein_id": "XP_024304728.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 703,
"cds_start": 1015,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 3119,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.784G>C",
"hgvs_p": "p.Ala262Pro",
"transcript": "XM_006719063.4",
"protein_id": "XP_006719126.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 626,
"cds_start": 784,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 801,
"cdna_end": null,
"cdna_length": 2745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"hgvs_c": "c.1015G>C",
"hgvs_p": "p.Ala339Pro",
"transcript": "XM_017019245.3",
"protein_id": "XP_016874734.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 392,
"cds_start": 1015,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 1270,
"cdna_end": null,
"cdna_length": 1893,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285854",
"gene_hgnc_id": null,
"hgvs_c": "n.942G>C",
"hgvs_p": null,
"transcript": "ENST00000648372.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GYS2",
"gene_hgnc_id": 4707,
"dbsnp": "rs121918421",
"frequency_reference_population": 0.000021089352,
"hom_count_reference_population": 0,
"allele_count_reference_population": 34,
"gnomad_exomes_af": 0.0000191778,
"gnomad_genomes_af": 0.0000394296,
"gnomad_exomes_ac": 28,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9428772330284119,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.771,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9455,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.26,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.129,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000261195.3",
"gene_symbol": "GYS2",
"hgnc_id": 4707,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1015G>C",
"hgvs_p": "p.Ala339Pro"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000647960.1",
"gene_symbol": "ENSG00000285854",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*1017G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Glycogen storage disorder due to hepatic glycogen synthase deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 LP:1",
"phenotype_combined": "Glycogen storage disorder due to hepatic glycogen synthase deficiency|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}