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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: 19-48969786-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48969786&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "GYS1",
"hgnc_id": 4706,
"hgvs_c": "c.1879G>A",
"hgvs_p": "p.Glu627Lys",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_002103.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 23,
"alphamissense_prediction": null,
"alphamissense_score": 0.1135,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Glycogen storage disease due to muscle and heart glycogen synthase deficiency,Inborn genetic diseases",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.15410414338111877,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 737,
"aa_ref": "E",
"aa_start": 627,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3569,
"cdna_start": 2076,
"cds_end": null,
"cds_length": 2214,
"cds_start": 1879,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_002103.5",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1879G>A",
"hgvs_p": "p.Glu627Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000323798.8",
"protein_coding": true,
"protein_id": "NP_002094.2",
"strand": false,
"transcript": "NM_002103.5",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 737,
"aa_ref": "E",
"aa_start": 627,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3569,
"cdna_start": 2076,
"cds_end": null,
"cds_length": 2214,
"cds_start": 1879,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000323798.8",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1879G>A",
"hgvs_p": "p.Glu627Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002103.5",
"protein_coding": true,
"protein_id": "ENSP00000317904.3",
"strand": false,
"transcript": "ENST00000323798.8",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 673,
"aa_ref": "E",
"aa_start": 563,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3378,
"cdna_start": 1885,
"cds_end": null,
"cds_length": 2022,
"cds_start": 1687,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000263276.6",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1687G>A",
"hgvs_p": "p.Glu563Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000263276.6",
"strand": false,
"transcript": "ENST00000263276.6",
"transcript_support_level": 1
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 759,
"aa_ref": "E",
"aa_start": 649,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3628,
"cdna_start": 2140,
"cds_end": null,
"cds_length": 2280,
"cds_start": 1945,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000960032.1",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1945G>A",
"hgvs_p": "p.Glu649Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630091.1",
"strand": false,
"transcript": "ENST00000960032.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 745,
"aa_ref": "E",
"aa_start": 635,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3616,
"cdna_start": 2128,
"cds_end": null,
"cds_length": 2238,
"cds_start": 1903,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000960031.1",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1903G>A",
"hgvs_p": "p.Glu635Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630090.1",
"strand": false,
"transcript": "ENST00000960031.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 689,
"aa_ref": "E",
"aa_start": 579,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3368,
"cdna_start": 1877,
"cds_end": null,
"cds_length": 2070,
"cds_start": 1735,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000960033.1",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1735G>A",
"hgvs_p": "p.Glu579Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000630092.1",
"strand": false,
"transcript": "ENST00000960033.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 675,
"aa_ref": "E",
"aa_start": 565,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3332,
"cdna_start": 1835,
"cds_end": null,
"cds_length": 2028,
"cds_start": 1693,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000917526.1",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1693G>A",
"hgvs_p": "p.Glu565Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587585.1",
"strand": false,
"transcript": "ENST00000917526.1",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 673,
"aa_ref": "E",
"aa_start": 563,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3377,
"cdna_start": 1884,
"cds_end": null,
"cds_length": 2022,
"cds_start": 1687,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NM_001161587.2",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1687G>A",
"hgvs_p": "p.Glu563Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001155059.1",
"strand": false,
"transcript": "NM_001161587.2",
"transcript_support_level": null
},
{
"aa_alt": "K",
"aa_end": null,
"aa_length": 483,
"aa_ref": "E",
"aa_start": 373,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2812,
"cdna_start": 1314,
"cds_end": null,
"cds_length": 1452,
"cds_start": 1117,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000917525.1",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "c.1117G>A",
"hgvs_p": "p.Glu373Lys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000587584.1",
"strand": false,
"transcript": "ENST00000917525.1",
"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": 3387,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "NR_027763.2",
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"hgvs_c": "n.1894G>A",
"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": "NR_027763.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs962330001",
"effect": "missense_variant",
"frequency_reference_population": 0.00001425174,
"gene_hgnc_id": 4706,
"gene_symbol": "GYS1",
"gnomad_exomes_ac": 15,
"gnomad_exomes_af": 0.0000102626,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.0000525548,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Glycogen storage disease due to muscle and heart glycogen synthase deficiency|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.233,
"pos": 48969786,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.252,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002103.5"
}
]
}