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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: 13-23203888-CAGTA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=23203888&ref=CAGTA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 23203888,
"ref": "CAGTA",
"alt": "C",
"effect": "frameshift_variant,splice_donor_variant,splice_region_variant,intron_variant",
"transcript": "ENST00000218867.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.195+4_195+7delAGTA",
"hgvs_p": null,
"transcript": "NM_000231.3",
"protein_id": "NP_000222.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 291,
"cds_start": -4,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1594,
"mane_select": "ENST00000218867.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.195_195+3delAGTA",
"hgvs_p": "p.Ala66fs",
"transcript": "ENST00000218867.4",
"protein_id": "ENSP00000218867.3",
"transcript_support_level": 1,
"aa_start": 65,
"aa_end": null,
"aa_length": 291,
"cds_start": 195,
"cds_end": null,
"cds_length": 876,
"cdna_start": 292,
"cdna_end": null,
"cdna_length": 1594,
"mane_select": "NM_000231.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.249+4_249+7delAGTA",
"hgvs_p": null,
"transcript": "NM_001378244.1",
"protein_id": "NP_001365173.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 309,
"cds_start": -4,
"cds_end": null,
"cds_length": 930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.195+4_195+7delAGTA",
"hgvs_p": null,
"transcript": "NM_001378245.1",
"protein_id": "NP_001365174.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 291,
"cds_start": -4,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.195+4_195+7delAGTA",
"hgvs_p": null,
"transcript": "NM_001378246.1",
"protein_id": "NP_001365175.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 291,
"cds_start": -4,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"hgvs_c": "c.55-30718_55-30715delAGTA",
"hgvs_p": null,
"transcript": "XM_047430542.1",
"protein_id": "XP_047286498.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 244,
"cds_start": -4,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SGCG",
"gene_hgnc_id": 10809,
"dbsnp": "rs797045106",
"frequency_reference_population": 0.000036441226,
"hom_count_reference_population": 0,
"allele_count_reference_population": 58,
"gnomad_exomes_af": 0.0000368198,
"gnomad_genomes_af": 0.0000328597,
"gnomad_exomes_ac": 53,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.9800000190734863,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.065,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000218867.4",
"gene_symbol": "SGCG",
"hgnc_id": 10809,
"effects": [
"frameshift_variant",
"splice_donor_variant",
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.195_195+3delAGTA",
"hgvs_p": "p.Ala66fs"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2C,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2C|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}