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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: 19-48969431-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=48969431&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 48969431,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_002103.5",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.2071C>G",
"hgvs_p": "p.Pro691Ala",
"transcript": "NM_002103.5",
"protein_id": "NP_002094.2",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 737,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000323798.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002103.5"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.2071C>G",
"hgvs_p": "p.Pro691Ala",
"transcript": "ENST00000323798.8",
"protein_id": "ENSP00000317904.3",
"transcript_support_level": 1,
"aa_start": 691,
"aa_end": null,
"aa_length": 737,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002103.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000323798.8"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1879C>G",
"hgvs_p": "p.Pro627Ala",
"transcript": "ENST00000263276.6",
"protein_id": "ENSP00000263276.6",
"transcript_support_level": 1,
"aa_start": 627,
"aa_end": null,
"aa_length": 673,
"cds_start": 1879,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263276.6"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.2137C>G",
"hgvs_p": "p.Pro713Ala",
"transcript": "ENST00000960032.1",
"protein_id": "ENSP00000630091.1",
"transcript_support_level": null,
"aa_start": 713,
"aa_end": null,
"aa_length": 759,
"cds_start": 2137,
"cds_end": null,
"cds_length": 2280,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960032.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.2095C>G",
"hgvs_p": "p.Pro699Ala",
"transcript": "ENST00000960031.1",
"protein_id": "ENSP00000630090.1",
"transcript_support_level": null,
"aa_start": 699,
"aa_end": null,
"aa_length": 745,
"cds_start": 2095,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960031.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1927C>G",
"hgvs_p": "p.Pro643Ala",
"transcript": "ENST00000960033.1",
"protein_id": "ENSP00000630092.1",
"transcript_support_level": null,
"aa_start": 643,
"aa_end": null,
"aa_length": 689,
"cds_start": 1927,
"cds_end": null,
"cds_length": 2070,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960033.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1885C>G",
"hgvs_p": "p.Pro629Ala",
"transcript": "ENST00000917526.1",
"protein_id": "ENSP00000587585.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 675,
"cds_start": 1885,
"cds_end": null,
"cds_length": 2028,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917526.1"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1879C>G",
"hgvs_p": "p.Pro627Ala",
"transcript": "NM_001161587.2",
"protein_id": "NP_001155059.1",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 673,
"cds_start": 1879,
"cds_end": null,
"cds_length": 2022,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001161587.2"
},
{
"aa_ref": "P",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "c.1309C>G",
"hgvs_p": "p.Pro437Ala",
"transcript": "ENST00000917525.1",
"protein_id": "ENSP00000587584.1",
"transcript_support_level": null,
"aa_start": 437,
"aa_end": null,
"aa_length": 483,
"cds_start": 1309,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000917525.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"hgvs_c": "n.2086C>G",
"hgvs_p": null,
"transcript": "NR_027763.2",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_027763.2"
}
],
"gene_symbol": "GYS1",
"gene_hgnc_id": 4706,
"dbsnp": "rs5453",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.256844162940979,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.182,
"revel_prediction": "Benign",
"alphamissense_score": 0.09,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.507,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_002103.5",
"gene_symbol": "GYS1",
"hgnc_id": 4706,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2071C>G",
"hgvs_p": "p.Pro691Ala"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}