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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: 5-151287372-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=151287372&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 151287372,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000335230.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.582G>T",
"hgvs_p": "p.Leu194Leu",
"transcript": "NM_181774.4",
"protein_id": "NP_861439.3",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 470,
"cds_start": 582,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 994,
"cdna_end": null,
"cdna_length": 2860,
"mane_select": "ENST00000335230.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.582G>T",
"hgvs_p": "p.Leu194Leu",
"transcript": "ENST00000335230.8",
"protein_id": "ENSP00000334750.3",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 470,
"cds_start": 582,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 994,
"cdna_end": null,
"cdna_length": 2860,
"mane_select": "NM_181774.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.705G>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "ENST00000377713.3",
"protein_id": "ENSP00000366942.3",
"transcript_support_level": 1,
"aa_start": 235,
"aa_end": null,
"aa_length": 511,
"cds_start": 705,
"cds_end": null,
"cds_length": 1536,
"cdna_start": 847,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.616G>T",
"hgvs_p": "p.Asp206Tyr",
"transcript": "XM_011537634.3",
"protein_id": "XP_011535936.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 249,
"cds_start": 616,
"cds_end": null,
"cds_length": 750,
"cdna_start": 1028,
"cdna_end": null,
"cdna_length": 1262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.705G>T",
"hgvs_p": "p.Leu235Leu",
"transcript": "NM_001145017.2",
"protein_id": "NP_001138489.1",
"transcript_support_level": null,
"aa_start": 235,
"aa_end": null,
"aa_length": 511,
"cds_start": 705,
"cds_end": null,
"cds_length": 1536,
"cdna_start": 1117,
"cdna_end": null,
"cdna_length": 2983,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.582G>T",
"hgvs_p": "p.Leu194Leu",
"transcript": "XM_011537627.4",
"protein_id": "XP_011535929.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 444,
"cds_start": 582,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 994,
"cdna_end": null,
"cdna_length": 2782,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.237G>T",
"hgvs_p": "p.Leu79Leu",
"transcript": "XM_011537630.3",
"protein_id": "XP_011535932.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 355,
"cds_start": 237,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 348,
"cdna_end": null,
"cdna_length": 2214,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.237G>T",
"hgvs_p": "p.Leu79Leu",
"transcript": "XM_011537631.3",
"protein_id": "XP_011535933.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 355,
"cds_start": 237,
"cds_end": null,
"cds_length": 1068,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "c.93G>T",
"hgvs_p": "p.Leu31Leu",
"transcript": "XM_011537633.2",
"protein_id": "XP_011535935.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 307,
"cds_start": 93,
"cds_end": null,
"cds_length": 924,
"cdna_start": 211,
"cdna_end": null,
"cdna_length": 2077,
"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": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"hgvs_c": "n.2482G>T",
"hgvs_p": null,
"transcript": "ENST00000423071.2",
"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": 3558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC36A3",
"gene_hgnc_id": 19659,
"dbsnp": "rs375396",
"frequency_reference_population": 0.19796564,
"hom_count_reference_population": 34903,
"allele_count_reference_population": 319492,
"gnomad_exomes_af": 0.197081,
"gnomad_genomes_af": 0.206469,
"gnomad_exomes_ac": 288105,
"gnomad_genomes_ac": 31387,
"gnomad_exomes_homalt": 31411,
"gnomad_genomes_homalt": 3492,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.374,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "ENST00000335230.8",
"gene_symbol": "SLC36A3",
"hgnc_id": 19659,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.582G>T",
"hgvs_p": "p.Leu194Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}