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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: 17-39672852-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=39672852&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 39672852,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000300658.9",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.914A>G",
"hgvs_p": "p.Asp305Gly",
"transcript": "NM_033419.5",
"protein_id": "NP_219487.3",
"transcript_support_level": null,
"aa_start": 305,
"aa_end": null,
"aa_length": 320,
"cds_start": 914,
"cds_end": null,
"cds_length": 963,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 2687,
"mane_select": "ENST00000300658.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.914A>G",
"hgvs_p": "p.Asp305Gly",
"transcript": "ENST00000300658.9",
"protein_id": "ENSP00000300658.4",
"transcript_support_level": 1,
"aa_start": 305,
"aa_end": null,
"aa_length": 320,
"cds_start": 914,
"cds_end": null,
"cds_length": 963,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 2687,
"mane_select": "NM_033419.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.447A>G",
"hgvs_p": "p.Ter149Trpext*?",
"transcript": "NM_001291733.2",
"protein_id": "NP_001278662.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 148,
"cds_start": 447,
"cds_end": null,
"cds_length": 447,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 2220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "*",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.447A>G",
"hgvs_p": "p.Ter149Trpext*?",
"transcript": "ENST00000579146.5",
"protein_id": "ENSP00000463234.1",
"transcript_support_level": 2,
"aa_start": 149,
"aa_end": null,
"aa_length": 148,
"cds_start": 447,
"cds_end": null,
"cds_length": 447,
"cdna_start": 490,
"cdna_end": null,
"cdna_length": 2220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.851A>G",
"hgvs_p": "p.Asp284Gly",
"transcript": "NM_001291728.2",
"protein_id": "NP_001278657.1",
"transcript_support_level": null,
"aa_start": 284,
"aa_end": null,
"aa_length": 299,
"cds_start": 851,
"cds_end": null,
"cds_length": 900,
"cdna_start": 894,
"cdna_end": null,
"cdna_length": 2624,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.851A>G",
"hgvs_p": "p.Asp284Gly",
"transcript": "ENST00000429199.6",
"protein_id": "ENSP00000415765.2",
"transcript_support_level": 2,
"aa_start": 284,
"aa_end": null,
"aa_length": 299,
"cds_start": 851,
"cds_end": null,
"cds_length": 900,
"cdna_start": 894,
"cdna_end": null,
"cdna_length": 970,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.761A>G",
"hgvs_p": "p.Asp254Gly",
"transcript": "NM_001291726.2",
"protein_id": "NP_001278655.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 269,
"cds_start": 761,
"cds_end": null,
"cds_length": 810,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 2534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.761A>G",
"hgvs_p": "p.Asp254Gly",
"transcript": "ENST00000378011.8",
"protein_id": "ENSP00000367250.4",
"transcript_support_level": 2,
"aa_start": 254,
"aa_end": null,
"aa_length": 269,
"cds_start": 761,
"cds_end": null,
"cds_length": 810,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 2533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.572A>G",
"hgvs_p": "p.Asp191Gly",
"transcript": "NM_001291730.2",
"protein_id": "NP_001278659.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 206,
"cds_start": 572,
"cds_end": null,
"cds_length": 621,
"cdna_start": 615,
"cdna_end": null,
"cdna_length": 2345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.509A>G",
"hgvs_p": "p.Asp170Gly",
"transcript": "NM_001291732.2",
"protein_id": "NP_001278661.1",
"transcript_support_level": null,
"aa_start": 170,
"aa_end": null,
"aa_length": 185,
"cds_start": 509,
"cds_end": null,
"cds_length": 558,
"cdna_start": 552,
"cdna_end": null,
"cdna_length": 2282,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.709A>G",
"hgvs_p": "p.Thr237Ala",
"transcript": "XM_011525480.2",
"protein_id": "XP_011523782.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 241,
"cds_start": 709,
"cds_end": null,
"cds_length": 726,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 2482,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.569A>G",
"hgvs_p": "p.Asp190Gly",
"transcript": "XM_047437082.1",
"protein_id": "XP_047293038.1",
"transcript_support_level": null,
"aa_start": 190,
"aa_end": null,
"aa_length": 205,
"cds_start": 569,
"cds_end": null,
"cds_length": 618,
"cdna_start": 714,
"cdna_end": null,
"cdna_length": 2444,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "n.1299A>G",
"hgvs_p": null,
"transcript": "ENST00000309862.10",
"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": 3028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"hgvs_c": "c.-161A>G",
"hgvs_p": null,
"transcript": "ENST00000619169.4",
"protein_id": "ENSP00000478028.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 240,
"cds_start": -4,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2094,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PGAP3",
"gene_hgnc_id": 23719,
"dbsnp": "rs587777252",
"frequency_reference_population": 0.00006505584,
"hom_count_reference_population": 0,
"allele_count_reference_population": 105,
"gnomad_exomes_af": 0.00006704,
"gnomad_genomes_af": 0.000045997,
"gnomad_exomes_ac": 98,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9414380788803101,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.817,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9615,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.51,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000300658.9",
"gene_symbol": "PGAP3",
"hgnc_id": 23719,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.914A>G",
"hgvs_p": "p.Asp305Gly"
}
],
"clinvar_disease": "Hyperphosphatasia with intellectual disability syndrome 4,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"phenotype_combined": "Hyperphosphatasia with intellectual disability syndrome 4|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}