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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: 3-119654544-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=119654544&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "POPDC2",
"hgnc_id": 17648,
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_001369919.2",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "COX17",
"hgnc_id": 2264,
"hgvs_c": "n.*345G>T",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "ENST00000490145.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": 0.993,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.08,
"chr": "3",
"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": 0.8854131698608398,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 368,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1822,
"cdna_start": 727,
"cds_end": null,
"cds_length": 1107,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001369919.2",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000493094.6",
"protein_coding": true,
"protein_id": "NP_001356848.1",
"strand": false,
"transcript": "NM_001369919.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 368,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1822,
"cdna_start": 727,
"cds_end": null,
"cds_length": 1107,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000493094.6",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001369919.2",
"protein_coding": true,
"protein_id": "ENSP00000417250.1",
"strand": false,
"transcript": "ENST00000493094.6",
"transcript_support_level": 5
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 364,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1679,
"cdna_start": 728,
"cds_end": null,
"cds_length": 1095,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000264231.7",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000264231.3",
"strand": false,
"transcript": "ENST00000264231.7",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 360,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1345,
"cdna_start": 728,
"cds_end": null,
"cds_length": 1083,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000468801.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000420715.1",
"strand": false,
"transcript": "ENST00000468801.1",
"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": 1309,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000474523.5",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "n.275G>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": "ENST00000474523.5",
"transcript_support_level": 1
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 368,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3568,
"cdna_start": 2012,
"cds_end": null,
"cds_length": 1107,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000866167.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000536226.1",
"strand": false,
"transcript": "ENST00000866167.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 368,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1813,
"cdna_start": 726,
"cds_end": null,
"cds_length": 1107,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000949666.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619725.1",
"strand": false,
"transcript": "ENST00000949666.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 364,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1681,
"cdna_start": 727,
"cds_end": null,
"cds_length": 1095,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_022135.4",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_071418.2",
"strand": false,
"transcript": "NM_022135.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 360,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1764,
"cdna_start": 727,
"cds_end": null,
"cds_length": 1083,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001308333.2",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001295262.1",
"strand": false,
"transcript": "NM_001308333.2",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 368,
"aa_ref": "E",
"aa_start": 187,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1399,
"cdna_start": 727,
"cds_end": null,
"cds_length": 1107,
"cds_start": 561,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "XM_047448703.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.561G>T",
"hgvs_p": "p.Glu187Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304659.1",
"strand": false,
"transcript": "XM_047448703.1",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 182,
"aa_ref": "E",
"aa_start": 5,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1519,
"cdna_start": 565,
"cds_end": null,
"cds_length": 549,
"cds_start": 15,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047448704.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "c.15G>T",
"hgvs_p": "p.Glu5Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304660.1",
"strand": false,
"transcript": "XM_047448704.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1958,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000341124.9",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "n.561G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000340753.5",
"strand": false,
"transcript": "ENST00000341124.9",
"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": 534,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000463323.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "n.267G>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": "ENST00000463323.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 492,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000476092.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "n.184G>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": "ENST00000476092.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 513,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000490145.1",
"gene_hgnc_id": 2264,
"gene_symbol": "COX17",
"hgvs_c": "n.*345G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000420406.1",
"strand": false,
"transcript": "ENST00000490145.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 513,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000490145.1",
"gene_hgnc_id": 2264,
"gene_symbol": "COX17",
"hgvs_c": "n.*345G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000420406.1",
"strand": false,
"transcript": "ENST00000490145.1",
"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": 946,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000468916.1",
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"hgvs_c": "n.655+5389G>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": "ENST00000468916.1",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 17648,
"gene_symbol": "POPDC2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"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": "Benign",
"phylop100way_score": 0.14,
"pos": 119654544,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.365,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001369919.2"
}
]
}