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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: 11-63590148-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=63590148&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 63590148,
"ref": "G",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_007069.3",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "NM_001128203.2",
"protein_id": "NP_001121675.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000415826.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128203.2"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000415826.3",
"protein_id": "ENSP00000389124.1",
"transcript_support_level": 2,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001128203.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000415826.3"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000323646.9",
"protein_id": "ENSP00000320337.5",
"transcript_support_level": 1,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000323646.9"
},
{
"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": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "n.433C>A",
"hgvs_p": null,
"transcript": "ENST00000394613.3",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000394613.3"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000873644.1",
"protein_id": "ENSP00000543703.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 196,
"cds_start": 339,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873644.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000911545.1",
"protein_id": "ENSP00000581604.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 196,
"cds_start": 339,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911545.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.432C>A",
"hgvs_p": "p.Cys144*",
"transcript": "ENST00000873646.1",
"protein_id": "ENSP00000543705.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 193,
"cds_start": 432,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873646.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.432C>A",
"hgvs_p": "p.Cys144*",
"transcript": "ENST00000873647.1",
"protein_id": "ENSP00000543706.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 193,
"cds_start": 432,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873647.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.411C>A",
"hgvs_p": "p.Cys137*",
"transcript": "ENST00000873643.1",
"protein_id": "ENSP00000543702.1",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 186,
"cds_start": 411,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873643.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "NM_007069.3",
"protein_id": "NP_009000.2",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007069.3"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000873645.1",
"protein_id": "ENSP00000543704.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873645.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000873648.1",
"protein_id": "ENSP00000543707.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000873648.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000911543.1",
"protein_id": "ENSP00000581602.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911543.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000911544.1",
"protein_id": "ENSP00000581603.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911544.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*",
"transcript": "ENST00000911547.1",
"protein_id": "ENSP00000581606.1",
"transcript_support_level": null,
"aa_start": 113,
"aa_end": null,
"aa_length": 162,
"cds_start": 339,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911547.1"
},
{
"aa_ref": "C",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.384C>A",
"hgvs_p": "p.Cys128*",
"transcript": "XM_011544741.2",
"protein_id": "XP_011543043.1",
"transcript_support_level": null,
"aa_start": 128,
"aa_end": null,
"aa_length": 177,
"cds_start": 384,
"cds_end": null,
"cds_length": 534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544741.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.16-15102C>A",
"hgvs_p": null,
"transcript": "ENST00000911546.1",
"protein_id": "ENSP00000581605.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 38,
"cds_start": null,
"cds_end": null,
"cds_length": 117,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911546.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "c.*106C>A",
"hgvs_p": null,
"transcript": "ENST00000540943.1",
"protein_id": "ENSP00000442576.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 26,
"cds_start": null,
"cds_end": null,
"cds_length": 83,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540943.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"hgvs_c": "n.*191C>A",
"hgvs_p": null,
"transcript": "ENST00000544269.1",
"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": "ENST00000544269.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC105369335",
"gene_hgnc_id": null,
"hgvs_c": "n.*58G>T",
"hgvs_p": null,
"transcript": "XR_950179.3",
"protein_id": null,
"transcript_support_level": null,
"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": "XR_950179.3"
}
],
"gene_symbol": "PLAAT3",
"gene_hgnc_id": 17825,
"dbsnp": "rs373632324",
"frequency_reference_population": 0.0000065695253,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000656953,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5299999713897705,
"computational_prediction_selected": "Pathogenic",
"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": 0.53,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": -0.857,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_007069.3",
"gene_symbol": "PLAAT3",
"hgnc_id": 17825,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.339C>A",
"hgvs_p": "p.Cys113*"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_950179.3",
"gene_symbol": "LOC105369335",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*58G>T",
"hgvs_p": null
}
],
"clinvar_disease": " familial partial, type 9,Lipodystrophy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Lipodystrophy, familial partial, type 9",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}