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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: 3-45775926-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=45775926&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 45775926,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000358525.9",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "NM_020208.4",
"protein_id": "NP_064593.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 592,
"cds_start": 417,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 534,
"cdna_end": null,
"cdna_length": 5425,
"mane_select": "ENST00000358525.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "ENST00000358525.9",
"protein_id": "ENSP00000346298.4",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 592,
"cds_start": 417,
"cds_end": null,
"cds_length": 1779,
"cdna_start": 534,
"cdna_end": null,
"cdna_length": 5425,
"mane_select": "NM_020208.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "ENST00000353278.8",
"protein_id": "ENSP00000296133.5",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 555,
"cds_start": 417,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 468,
"cdna_end": null,
"cdna_length": 5247,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "NM_001385683.1",
"protein_id": "NP_001372612.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 603,
"cds_start": 417,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 534,
"cdna_end": null,
"cdna_length": 5458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "ENST00000703343.1",
"protein_id": "ENSP00000515266.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 603,
"cds_start": 417,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 572,
"cdna_end": null,
"cdna_length": 3000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "NM_022405.4",
"protein_id": "NP_071800.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 555,
"cds_start": 417,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 534,
"cdna_end": null,
"cdna_length": 5314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "NM_001406066.1",
"protein_id": "NP_001392995.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 547,
"cds_start": 417,
"cds_end": null,
"cds_length": 1644,
"cdna_start": 534,
"cdna_end": null,
"cdna_length": 4749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.276T>C",
"hgvs_p": "p.Cys92Cys",
"transcript": "NM_001406067.1",
"protein_id": "NP_001392996.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 545,
"cds_start": 276,
"cds_end": null,
"cds_length": 1638,
"cdna_start": 393,
"cdna_end": null,
"cdna_length": 5284,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys",
"transcript": "NM_001406069.1",
"protein_id": "NP_001392998.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 510,
"cds_start": 417,
"cds_end": null,
"cds_length": 1533,
"cdna_start": 534,
"cdna_end": null,
"cdna_length": 4638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "c.120T>C",
"hgvs_p": "p.Cys40Cys",
"transcript": "XM_011533847.3",
"protein_id": "XP_011532149.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 493,
"cds_start": 120,
"cds_end": null,
"cds_length": 1482,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 5741,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "n.392T>C",
"hgvs_p": null,
"transcript": "ENST00000413781.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 910,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "n.489T>C",
"hgvs_p": null,
"transcript": "ENST00000703344.1",
"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": 3086,
"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": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "n.534T>C",
"hgvs_p": null,
"transcript": "NR_176011.1",
"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": 5505,
"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": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"hgvs_c": "n.534T>C",
"hgvs_p": null,
"transcript": "NR_176012.1",
"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": 3946,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC6A20",
"gene_hgnc_id": 30927,
"dbsnp": "rs758386",
"frequency_reference_population": 0.9548059,
"hom_count_reference_population": 735934,
"allele_count_reference_population": 1541242,
"gnomad_exomes_af": 0.954286,
"gnomad_genomes_af": 0.9598,
"gnomad_exomes_ac": 1395051,
"gnomad_genomes_ac": 146191,
"gnomad_exomes_homalt": 665759,
"gnomad_genomes_homalt": 70175,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.325,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000358525.9",
"gene_symbol": "SLC6A20",
"hgnc_id": 30927,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.417T>C",
"hgvs_p": "p.Cys139Cys"
}
],
"clinvar_disease": "Hyperglycinuria,SLC6A20-related disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Hyperglycinuria|not provided|SLC6A20-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}