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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: 5-156759285-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=156759285&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 156759285,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000337851.9",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.768G>A",
"hgvs_p": "p.Thr256Thr",
"transcript": "NM_000337.6",
"protein_id": "NP_000328.2",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 290,
"cds_start": 768,
"cds_end": null,
"cds_length": 873,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 9383,
"mane_select": "ENST00000337851.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.768G>A",
"hgvs_p": "p.Thr256Thr",
"transcript": "ENST00000337851.9",
"protein_id": "ENSP00000338343.4",
"transcript_support_level": 1,
"aa_start": 256,
"aa_end": null,
"aa_length": 290,
"cds_start": 768,
"cds_end": null,
"cds_length": 873,
"cdna_start": 880,
"cdna_end": null,
"cdna_length": 9383,
"mane_select": "NM_000337.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.765G>A",
"hgvs_p": "p.Thr255Thr",
"transcript": "ENST00000435422.7",
"protein_id": "ENSP00000403003.2",
"transcript_support_level": 1,
"aa_start": 255,
"aa_end": null,
"aa_length": 289,
"cds_start": 765,
"cds_end": null,
"cds_length": 870,
"cdna_start": 1252,
"cdna_end": null,
"cdna_length": 9755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.765G>A",
"hgvs_p": "p.Thr255Thr",
"transcript": "NM_001128209.2",
"protein_id": "NP_001121681.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 289,
"cds_start": 765,
"cds_end": null,
"cds_length": 870,
"cdna_start": 834,
"cdna_end": null,
"cdna_length": 9337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.768G>A",
"hgvs_p": "p.Thr256Thr",
"transcript": "XM_005265966.6",
"protein_id": "XP_005266023.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 290,
"cds_start": 768,
"cds_end": null,
"cds_length": 873,
"cdna_start": 1113,
"cdna_end": null,
"cdna_length": 9616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.768G>A",
"hgvs_p": "p.Thr256Thr",
"transcript": "XM_017009724.2",
"protein_id": "XP_016865213.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 290,
"cds_start": 768,
"cds_end": null,
"cds_length": 873,
"cdna_start": 1725,
"cdna_end": null,
"cdna_length": 10228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.768G>A",
"hgvs_p": "p.Thr256Thr",
"transcript": "XM_047417518.1",
"protein_id": "XP_047273474.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 290,
"cds_start": 768,
"cds_end": null,
"cds_length": 873,
"cdna_start": 1864,
"cdna_end": null,
"cdna_length": 10367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.768G>A",
"hgvs_p": "p.Thr256Thr",
"transcript": "XM_047417519.1",
"protein_id": "XP_047273475.1",
"transcript_support_level": null,
"aa_start": 256,
"aa_end": null,
"aa_length": 290,
"cds_start": 768,
"cds_end": null,
"cds_length": 873,
"cdna_start": 2215,
"cdna_end": null,
"cdna_length": 10718,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"hgvs_c": "c.765G>A",
"hgvs_p": "p.Thr255Thr",
"transcript": "XM_047417520.1",
"protein_id": "XP_047273476.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 289,
"cds_start": 765,
"cds_end": null,
"cds_length": 870,
"cdna_start": 1609,
"cdna_end": null,
"cdna_length": 10112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SGCD",
"gene_hgnc_id": 10807,
"dbsnp": "rs376141942",
"frequency_reference_population": 0.000009916884,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000958086,
"gnomad_genomes_af": 0.0000131437,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.41999998688697815,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.063,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000337851.9",
"gene_symbol": "SGCD",
"hgnc_id": 10807,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.768G>A",
"hgvs_p": "p.Thr256Thr"
}
],
"clinvar_disease": "Autosomal recessive limb-girdle muscular dystrophy type 2F,Inborn genetic diseases,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:3",
"phenotype_combined": "not provided|Autosomal recessive limb-girdle muscular dystrophy type 2F|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}