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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: 12-98595490-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=98595490&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 98595490,
"ref": "G",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000552981.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Gly72Val",
"transcript": "NM_005888.4",
"protein_id": "NP_005879.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 362,
"cds_start": 215,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 274,
"cdna_end": null,
"cdna_length": 5987,
"mane_select": null,
"mane_plus": "ENST00000228318.8",
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Gly72Val",
"transcript": "ENST00000228318.8",
"protein_id": "ENSP00000228318.3",
"transcript_support_level": 5,
"aa_start": 72,
"aa_end": null,
"aa_length": 362,
"cds_start": 215,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 274,
"cdna_end": null,
"cdna_length": 5987,
"mane_select": null,
"mane_plus": "NM_005888.4",
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "n.1602G>T",
"hgvs_p": null,
"transcript": "ENST00000546766.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3236,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "n.215G>T",
"hgvs_p": null,
"transcript": "ENST00000551123.5",
"protein_id": "ENSP00000449009.1",
"transcript_support_level": 1,
"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": 1417,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "NM_002635.4",
"protein_id": "NP_002626.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 361,
"cds_start": -4,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5984,
"mane_select": "ENST00000552981.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "ENST00000552981.6",
"protein_id": "ENSP00000448708.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 361,
"cds_start": -4,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5984,
"mane_select": "NM_002635.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "ENST00000188376.9",
"protein_id": "ENSP00000188376.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 361,
"cds_start": -4,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "ENST00000401722.7",
"protein_id": "ENSP00000383898.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 361,
"cds_start": -4,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6087,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Gly72Val",
"transcript": "ENST00000551917.5",
"protein_id": "ENSP00000447310.1",
"transcript_support_level": 2,
"aa_start": 72,
"aa_end": null,
"aa_length": 362,
"cds_start": 215,
"cds_end": null,
"cds_length": 1089,
"cdna_start": 306,
"cdna_end": null,
"cdna_length": 1359,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.215G>T",
"hgvs_p": "p.Gly72Val",
"transcript": "ENST00000550695.1",
"protein_id": "ENSP00000449479.1",
"transcript_support_level": 3,
"aa_start": 72,
"aa_end": null,
"aa_length": 153,
"cds_start": 215,
"cds_end": null,
"cds_length": 463,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "NM_213611.3",
"protein_id": "NP_998776.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 361,
"cds_start": -4,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "ENST00000549338.5",
"protein_id": "ENSP00000447740.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 361,
"cds_start": -4,
"cds_end": null,
"cds_length": 1086,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "ENST00000548847.1",
"protein_id": "ENSP00000449166.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": -4,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "c.158-237G>T",
"hgvs_p": null,
"transcript": "ENST00000547534.5",
"protein_id": "ENSP00000449793.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 156,
"cds_start": -4,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 556,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"hgvs_c": "n.-174G>T",
"hgvs_p": null,
"transcript": "ENST00000547908.1",
"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": 893,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC25A3",
"gene_hgnc_id": 10989,
"dbsnp": "rs104894375",
"frequency_reference_population": 6.842669e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84267e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9776632785797119,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.909,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9981,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.49,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 10.003,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000552981.6",
"gene_symbol": "SLC25A3",
"hgnc_id": 10989,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.158-237G>T",
"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
}