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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: 13-51739103-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=51739103&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": "WDFY2",
"hgnc_id": 20482,
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Ser218Asn",
"inheritance_mode": "AR",
"pathogenic_score": 6,
"score": 6,
"transcript": "NM_052950.4",
"verdict": "Likely_pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "LOC124903177",
"hgnc_id": null,
"hgvs_c": "n.-5C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 6,
"score": 6,
"transcript": "XR_007063807.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_score": 6,
"allele_count_reference_population": 22,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9766,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.1,
"chr": "13",
"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": 0.9596840143203735,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 400,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9369,
"cdna_start": 879,
"cds_end": null,
"cds_length": 1203,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_052950.4",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Ser218Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000298125.7",
"protein_coding": true,
"protein_id": "NP_443182.1",
"strand": true,
"transcript": "NM_052950.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 400,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9369,
"cdna_start": 879,
"cds_end": null,
"cds_length": 1203,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000298125.7",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Ser218Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_052950.4",
"protein_coding": true,
"protein_id": "ENSP00000298125.4",
"strand": true,
"transcript": "ENST00000298125.7",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 409,
"aa_ref": "S",
"aa_start": 227,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2163,
"cdna_start": 906,
"cds_end": null,
"cds_length": 1230,
"cds_start": 680,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000923033.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.680G>A",
"hgvs_p": "p.Ser227Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000593092.1",
"strand": true,
"transcript": "ENST00000923033.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 406,
"aa_ref": "S",
"aa_start": 224,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3202,
"cdna_start": 897,
"cds_end": null,
"cds_length": 1221,
"cds_start": 671,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000876143.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.671G>A",
"hgvs_p": "p.Ser224Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546202.1",
"strand": true,
"transcript": "ENST00000876143.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 400,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8333,
"cdna_start": 753,
"cds_end": null,
"cds_length": 1203,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000923031.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Ser218Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000593090.1",
"strand": true,
"transcript": "ENST00000923031.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 398,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3027,
"cdna_start": 879,
"cds_end": null,
"cds_length": 1197,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000923032.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Ser218Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000593091.1",
"strand": true,
"transcript": "ENST00000923032.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 357,
"aa_ref": "S",
"aa_start": 175,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1359,
"cdna_start": 721,
"cds_end": null,
"cds_length": 1074,
"cds_start": 524,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000944288.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.524G>A",
"hgvs_p": "p.Ser175Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000614347.1",
"strand": true,
"transcript": "ENST00000944288.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 312,
"aa_ref": "S",
"aa_start": 130,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2452,
"cdna_start": 615,
"cds_end": null,
"cds_length": 939,
"cds_start": 389,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000876144.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.389G>A",
"hgvs_p": "p.Ser130Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546203.1",
"strand": true,
"transcript": "ENST00000876144.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 269,
"aa_ref": "S",
"aa_start": 87,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1638,
"cdna_start": 405,
"cds_end": null,
"cds_length": 810,
"cds_start": 260,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000944287.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.260G>A",
"hgvs_p": "p.Ser87Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000614346.1",
"strand": true,
"transcript": "ENST00000944287.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 398,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5834,
"cdna_start": 879,
"cds_end": null,
"cds_length": 1197,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011534914.2",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Ser218Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011533216.1",
"strand": true,
"transcript": "XM_011534914.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 334,
"aa_ref": "S",
"aa_start": 152,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10824,
"cdna_start": 2334,
"cds_end": null,
"cds_length": 1005,
"cds_start": 455,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_024449317.2",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.455G>A",
"hgvs_p": "p.Ser152Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024305085.1",
"strand": true,
"transcript": "XM_024449317.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 311,
"aa_ref": "S",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9295,
"cdna_start": 805,
"cds_end": null,
"cds_length": 936,
"cds_start": 386,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_011534915.3",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.386G>A",
"hgvs_p": "p.Ser129Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011533217.1",
"strand": true,
"transcript": "XM_011534915.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 311,
"aa_ref": "S",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10750,
"cdna_start": 2260,
"cds_end": null,
"cds_length": 936,
"cds_start": 386,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047430088.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.386G>A",
"hgvs_p": "p.Ser129Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286044.1",
"strand": true,
"transcript": "XM_047430088.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 290,
"aa_ref": "S",
"aa_start": 218,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1227,
"cdna_start": 879,
"cds_end": null,
"cds_length": 873,
"cds_start": 653,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047430089.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.653G>A",
"hgvs_p": "p.Ser218Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286045.1",
"strand": true,
"transcript": "XM_047430089.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 201,
"aa_ref": "S",
"aa_start": 129,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 790,
"cdna_start": 442,
"cds_end": null,
"cds_length": 606,
"cds_start": 386,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047430091.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "c.386G>A",
"hgvs_p": "p.Ser129Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047286047.1",
"strand": true,
"transcript": "XM_047430091.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4679,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XR_007063659.1",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "n.879G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007063659.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2060,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 13,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XR_941483.2",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "n.879G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_941483.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 395,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000460145.2",
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"hgvs_c": "n.-45G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000460145.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 287,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007063807.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC124903177",
"hgvs_c": "n.-5C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007063807.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1231082529",
"effect": "missense_variant",
"frequency_reference_population": 0.000013719491,
"gene_hgnc_id": 20482,
"gene_symbol": "WDFY2",
"gnomad_exomes_ac": 20,
"gnomad_exomes_af": 0.00001378,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131422,
"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": 5.353,
"pos": 51739103,
"ref": "G",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.581,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_052950.4"
}
]
}