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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: X-1389431-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=1389431&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 1389431,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_001636.4",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "NM_001636.4",
"protein_id": "NP_001627.2",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 298,
"cds_start": 408,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000381401.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001636.4"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000381401.11",
"protein_id": "ENSP00000370808.5",
"transcript_support_level": 1,
"aa_start": 136,
"aa_end": null,
"aa_length": 298,
"cds_start": 408,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001636.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000381401.11"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000871943.1",
"protein_id": "ENSP00000542002.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 324,
"cds_start": 408,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871943.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000871942.1",
"protein_id": "ENSP00000542001.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 298,
"cds_start": 408,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871942.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000936562.1",
"protein_id": "ENSP00000606621.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 298,
"cds_start": 408,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936562.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000966894.1",
"protein_id": "ENSP00000636953.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 298,
"cds_start": 408,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966894.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000966895.1",
"protein_id": "ENSP00000636954.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 298,
"cds_start": 408,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000966895.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.402C>T",
"hgvs_p": "p.Phe134Phe",
"transcript": "ENST00000871944.1",
"protein_id": "ENSP00000542003.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 296,
"cds_start": 402,
"cds_end": null,
"cds_length": 891,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000871944.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.390C>T",
"hgvs_p": "p.Phe130Phe",
"transcript": "ENST00000936564.1",
"protein_id": "ENSP00000606623.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 292,
"cds_start": 390,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936564.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.387C>T",
"hgvs_p": "p.Phe129Phe",
"transcript": "ENST00000936565.1",
"protein_id": "ENSP00000606624.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 291,
"cds_start": 387,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936565.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000936563.1",
"protein_id": "ENSP00000606622.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 251,
"cds_start": 408,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936563.1"
},
{
"aa_ref": "F",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe",
"transcript": "ENST00000936566.1",
"protein_id": "ENSP00000606625.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 227,
"cds_start": 408,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000936566.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "n.601C>T",
"hgvs_p": null,
"transcript": "ENST00000475167.6",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000475167.6"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"hgvs_c": "n.589C>T",
"hgvs_p": null,
"transcript": "ENST00000484026.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000484026.6"
}
],
"gene_symbol": "SLC25A6",
"gene_hgnc_id": 10992,
"dbsnp": "rs7205",
"frequency_reference_population": 0.26764026,
"hom_count_reference_population": 277630,
"allele_count_reference_population": 431791,
"gnomad_exomes_af": 0.263265,
"gnomad_genomes_af": 0.309674,
"gnomad_exomes_ac": 384692,
"gnomad_genomes_ac": 47099,
"gnomad_exomes_homalt": 52996,
"gnomad_genomes_homalt": 8165,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4300000071525574,
"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": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.093,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001636.4",
"gene_symbol": "SLC25A6",
"hgnc_id": 10992,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.408C>T",
"hgvs_p": "p.Phe136Phe"
}
],
"clinvar_disease": "SLC25A6-related disorder",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "SLC25A6-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}