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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: 5-79126212-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=79126212&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 79126212,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000274353.10",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.792C>T",
"hgvs_p": "p.Leu264Leu",
"transcript": "NM_001713.3",
"protein_id": "NP_001704.2",
"transcript_support_level": null,
"aa_start": 264,
"aa_end": null,
"aa_length": 406,
"cds_start": 792,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 869,
"cdna_end": null,
"cdna_length": 2470,
"mane_select": "ENST00000274353.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.792C>T",
"hgvs_p": "p.Leu264Leu",
"transcript": "ENST00000274353.10",
"protein_id": "ENSP00000274353.5",
"transcript_support_level": 1,
"aa_start": 264,
"aa_end": null,
"aa_length": 406,
"cds_start": 792,
"cds_end": null,
"cds_length": 1221,
"cdna_start": 869,
"cdna_end": null,
"cdna_length": 2470,
"mane_select": "NM_001713.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "c.333C>T",
"hgvs_p": "p.Leu111Leu",
"transcript": "ENST00000524080.1",
"protein_id": "ENSP00000428240.1",
"transcript_support_level": 2,
"aa_start": 111,
"aa_end": null,
"aa_length": 253,
"cds_start": 333,
"cds_end": null,
"cds_length": 762,
"cdna_start": 410,
"cdna_end": null,
"cdna_length": 1207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "n.252C>T",
"hgvs_p": null,
"transcript": "ENST00000521279.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"hgvs_c": "n.505C>T",
"hgvs_p": null,
"transcript": "ENST00000523508.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DMGDH",
"gene_hgnc_id": 24475,
"hgvs_c": "n.129-4860G>A",
"hgvs_p": null,
"transcript": "ENST00000518707.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DMGDH",
"gene_hgnc_id": 24475,
"hgvs_c": "n.229-4860G>A",
"hgvs_p": null,
"transcript": "ENST00000520388.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BHMT",
"gene_hgnc_id": 1047,
"dbsnp": "rs4703772",
"frequency_reference_population": 0.007110594,
"hom_count_reference_population": 969,
"allele_count_reference_population": 11473,
"gnomad_exomes_af": 0.00658017,
"gnomad_genomes_af": 0.0121996,
"gnomad_exomes_ac": 9615,
"gnomad_genomes_ac": 1858,
"gnomad_exomes_homalt": 834,
"gnomad_genomes_homalt": 135,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"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": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.154,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000274353.10",
"gene_symbol": "BHMT",
"hgnc_id": 1047,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.792C>T",
"hgvs_p": "p.Leu264Leu"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000518707.1",
"gene_symbol": "DMGDH",
"hgnc_id": 24475,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.129-4860G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}