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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: 9-101476144-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=101476144&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 101476144,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_032342.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "NM_032342.3",
"protein_id": "NP_115718.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1251,
"cdna_end": null,
"cdna_length": 4225,
"mane_select": "ENST00000374848.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "ENST00000374848.8",
"protein_id": "ENSP00000363981.3",
"transcript_support_level": 1,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1251,
"cdna_end": null,
"cdna_length": 4225,
"mane_select": "NM_032342.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "ENST00000374851.1",
"protein_id": "ENSP00000363984.1",
"transcript_support_level": 1,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 2097,
"cdna_end": null,
"cdna_length": 5070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "NM_001303107.2",
"protein_id": "NP_001290036.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1306,
"cdna_end": null,
"cdna_length": 4280,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "NM_001303108.2",
"protein_id": "NP_001290037.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 4203,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "NM_001371233.1",
"protein_id": "NP_001358162.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1239,
"cdna_end": null,
"cdna_length": 4213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "ENST00000374847.5",
"protein_id": "ENSP00000363980.1",
"transcript_support_level": 3,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1250,
"cdna_end": null,
"cdna_length": 4223,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp",
"transcript": "XM_024447701.2",
"protein_id": "XP_024303469.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 403,
"cds_start": 949,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 2195,
"cdna_end": null,
"cdna_length": 5169,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.212-3696G>A",
"hgvs_p": null,
"transcript": "ENST00000424154.6",
"protein_id": null,
"transcript_support_level": 3,
"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": 1132,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.243-3696G>A",
"hgvs_p": null,
"transcript": "ENST00000425734.1",
"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": 466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.300-5219G>A",
"hgvs_p": null,
"transcript": "ENST00000431507.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 439,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.314+1102G>A",
"hgvs_p": null,
"transcript": "ENST00000450109.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.337+1102G>A",
"hgvs_p": null,
"transcript": "NR_121573.1",
"protein_id": null,
"transcript_support_level": null,
"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": 565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.300-3696G>A",
"hgvs_p": null,
"transcript": "NR_121574.1",
"protein_id": null,
"transcript_support_level": null,
"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": 527,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.300-5219G>A",
"hgvs_p": null,
"transcript": "NR_121575.1",
"protein_id": null,
"transcript_support_level": null,
"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": 443,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TMEM246-AS1",
"gene_hgnc_id": 51191,
"hgvs_c": "n.171-3696G>A",
"hgvs_p": null,
"transcript": "NR_121576.1",
"protein_id": null,
"transcript_support_level": null,
"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": 398,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PGAP4",
"gene_hgnc_id": 28180,
"dbsnp": "rs766828805",
"frequency_reference_population": 0.000016417822,
"hom_count_reference_population": 0,
"allele_count_reference_population": 24,
"gnomad_exomes_af": 0.0000164178,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 24,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7754344940185547,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.418,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8139,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.57,
"phylop100way_prediction": "Uncertain_significance",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,PP3",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM1",
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_032342.3",
"gene_symbol": "PGAP4",
"hgnc_id": 28180,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.949C>T",
"hgvs_p": "p.Arg317Trp"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000425734.1",
"gene_symbol": "TMEM246-AS1",
"hgnc_id": 51191,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.243-3696G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}