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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: 12-110459811-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=110459811&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 110459811,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001164372.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.209G>A",
"hgvs_p": "p.Arg70Gln",
"transcript": "NM_016301.4",
"protein_id": "NP_057385.3",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 284,
"cds_start": 209,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000228827.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016301.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.209G>A",
"hgvs_p": "p.Arg70Gln",
"transcript": "ENST00000228827.8",
"protein_id": "ENSP00000228827.3",
"transcript_support_level": 1,
"aa_start": 70,
"aa_end": null,
"aa_length": 284,
"cds_start": 209,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016301.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000228827.8"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.239G>A",
"hgvs_p": "p.Arg80Gln",
"transcript": "ENST00000537466.6",
"protein_id": "ENSP00000443068.2",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 294,
"cds_start": 239,
"cds_end": null,
"cds_length": 885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537466.6"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.326G>A",
"hgvs_p": "p.Arg109Gln",
"transcript": "NM_001164372.2",
"protein_id": "NP_001157844.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 323,
"cds_start": 326,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164372.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.326G>A",
"hgvs_p": "p.Arg109Gln",
"transcript": "ENST00000543199.5",
"protein_id": "ENSP00000442770.1",
"transcript_support_level": 5,
"aa_start": 109,
"aa_end": null,
"aa_length": 323,
"cds_start": 326,
"cds_end": null,
"cds_length": 972,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000543199.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.239G>A",
"hgvs_p": "p.Arg80Gln",
"transcript": "NM_001164373.2",
"protein_id": "NP_001157845.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 294,
"cds_start": 239,
"cds_end": null,
"cds_length": 885,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001164373.2"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.143G>A",
"hgvs_p": "p.Arg48Gln",
"transcript": "ENST00000550974.1",
"protein_id": "ENSP00000447480.1",
"transcript_support_level": 5,
"aa_start": 48,
"aa_end": null,
"aa_length": 158,
"cds_start": 143,
"cds_end": null,
"cds_length": 477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000550974.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.50G>A",
"hgvs_p": "p.Arg17Gln",
"transcript": "ENST00000550228.5",
"protein_id": "ENSP00000448335.1",
"transcript_support_level": 3,
"aa_start": 17,
"aa_end": null,
"aa_length": 116,
"cds_start": 50,
"cds_end": null,
"cds_length": 351,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000550228.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.446G>A",
"hgvs_p": "p.Arg149Gln",
"transcript": "XM_047428933.1",
"protein_id": "XP_047284889.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 363,
"cds_start": 446,
"cds_end": null,
"cds_length": 1092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428933.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"transcript": "XM_047428934.1",
"protein_id": "XP_047284890.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 353,
"cds_start": 416,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428934.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.446G>A",
"hgvs_p": "p.Arg149Gln",
"transcript": "XM_047428935.1",
"protein_id": "XP_047284891.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 292,
"cds_start": 446,
"cds_end": null,
"cds_length": 879,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428935.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.416G>A",
"hgvs_p": "p.Arg139Gln",
"transcript": "XM_047428936.1",
"protein_id": "XP_047284892.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 282,
"cds_start": 416,
"cds_end": null,
"cds_length": 849,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428936.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.143G>A",
"hgvs_p": "p.Arg48Gln",
"transcript": "XM_017019394.2",
"protein_id": "XP_016874883.1",
"transcript_support_level": null,
"aa_start": 48,
"aa_end": null,
"aa_length": 262,
"cds_start": 143,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017019394.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "c.188-2177G>A",
"hgvs_p": null,
"transcript": "ENST00000912297.1",
"protein_id": "ENSP00000582356.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 238,
"cds_start": null,
"cds_end": null,
"cds_length": 717,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912297.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000300534",
"gene_hgnc_id": null,
"hgvs_c": "n.236C>T",
"hgvs_p": null,
"transcript": "ENST00000772597.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000772597.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"hgvs_c": "n.*9G>A",
"hgvs_p": null,
"transcript": "ENST00000552180.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000552180.5"
}
],
"gene_symbol": "GPN3",
"gene_hgnc_id": 30186,
"dbsnp": "rs748305243",
"frequency_reference_population": 0.000058250575,
"hom_count_reference_population": 0,
"allele_count_reference_population": 94,
"gnomad_exomes_af": 0.0000595257,
"gnomad_genomes_af": 0.000046003,
"gnomad_exomes_ac": 87,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06127822399139404,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.067,
"revel_prediction": "Benign",
"alphamissense_score": 0.1028,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.852,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001164372.2",
"gene_symbol": "GPN3",
"hgnc_id": 30186,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.326G>A",
"hgvs_p": "p.Arg109Gln"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000772597.1",
"gene_symbol": "ENSG00000300534",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.236C>T",
"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
}