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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: 11-63598127-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=63598127&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PLAAT3",
"hgnc_id": 17825,
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_007069.3",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 13,
"alphamissense_prediction": null,
"alphamissense_score": 0.757,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.18,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9415257573127747,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1075,
"cdna_start": 155,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001128203.2",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000415826.3",
"protein_coding": true,
"protein_id": "NP_001121675.1",
"strand": false,
"transcript": "NM_001128203.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1075,
"cdna_start": 155,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000415826.3",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001128203.2",
"protein_coding": true,
"protein_id": "ENSP00000389124.1",
"strand": false,
"transcript": "ENST00000415826.3",
"transcript_support_level": 2
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2594,
"cdna_start": 407,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000323646.9",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000320337.5",
"strand": false,
"transcript": "ENST00000323646.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 678,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000394613.3",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "n.160-14C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000394613.3",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 196,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2754,
"cdna_start": 442,
"cds_end": null,
"cds_length": 591,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000873644.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543703.1",
"strand": false,
"transcript": "ENST00000873644.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 196,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 890,
"cdna_start": 181,
"cds_end": null,
"cds_length": 591,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000911545.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581604.1",
"strand": false,
"transcript": "ENST00000911545.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 193,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2318,
"cdna_start": 191,
"cds_end": null,
"cds_length": 582,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000873646.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543705.1",
"strand": false,
"transcript": "ENST00000873646.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 193,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2594,
"cdna_start": 467,
"cds_end": null,
"cds_length": 582,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000873647.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543706.1",
"strand": false,
"transcript": "ENST00000873647.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 186,
"aa_ref": "R",
"aa_start": 42,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2428,
"cdna_start": 230,
"cds_end": null,
"cds_length": 561,
"cds_start": 124,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000873643.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.124C>T",
"hgvs_p": "p.Arg42Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543702.1",
"strand": false,
"transcript": "ENST00000873643.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1395,
"cdna_start": 475,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_007069.3",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_009000.2",
"strand": false,
"transcript": "NM_007069.3",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2307,
"cdna_start": 236,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000873645.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543704.1",
"strand": false,
"transcript": "ENST00000873645.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 815,
"cdna_start": 210,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000873648.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543707.1",
"strand": false,
"transcript": "ENST00000873648.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 838,
"cdna_start": 231,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000911543.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581602.1",
"strand": false,
"transcript": "ENST00000911543.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 888,
"cdna_start": 281,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000911544.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581603.1",
"strand": false,
"transcript": "ENST00000911544.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 162,
"aa_ref": "R",
"aa_start": 18,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 810,
"cdna_start": 203,
"cds_end": null,
"cds_length": 489,
"cds_start": 52,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000911547.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581606.1",
"strand": false,
"transcript": "ENST00000911547.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 177,
"aa_ref": "R",
"aa_start": 33,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1298,
"cdna_start": 378,
"cds_end": null,
"cds_length": 534,
"cds_start": 97,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_011544741.2",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.97C>T",
"hgvs_p": "p.Arg33Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011543043.1",
"strand": false,
"transcript": "XM_011544741.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 38,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 416,
"cdna_start": null,
"cds_end": null,
"cds_length": 117,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000911546.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.15+15873C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581605.1",
"strand": false,
"transcript": "ENST00000911546.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 26,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 243,
"cdna_start": null,
"cds_end": null,
"cds_length": 83,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000540943.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "c.-32-7759C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000442576.1",
"strand": false,
"transcript": "ENST00000540943.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 430,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000544269.1",
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"hgvs_c": "n.334C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000544269.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs761259464",
"effect": "missense_variant",
"frequency_reference_population": 0.000008055062,
"gene_hgnc_id": 17825,
"gene_symbol": "PLAAT3",
"gnomad_exomes_ac": 12,
"gnomad_exomes_af": 0.00000820959,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657091,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 3.817,
"pos": 63598127,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.523,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.25,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.25,
"transcript": "NM_007069.3"
}
]
}