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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: 2-201654839-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=201654839&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 201654839,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000409474.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1379C>T",
"hgvs_p": "p.Pro460Leu",
"transcript": "NM_033066.3",
"protein_id": "NP_149055.2",
"transcript_support_level": null,
"aa_start": 460,
"aa_end": null,
"aa_length": 637,
"cds_start": 1379,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1537,
"cdna_end": null,
"cdna_length": 2408,
"mane_select": "ENST00000409474.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1379C>T",
"hgvs_p": "p.Pro460Leu",
"transcript": "ENST00000409474.8",
"protein_id": "ENSP00000387278.3",
"transcript_support_level": 1,
"aa_start": 460,
"aa_end": null,
"aa_length": 637,
"cds_start": 1379,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1537,
"cdna_end": null,
"cdna_length": 2408,
"mane_select": "NM_033066.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"transcript": "ENST00000447335.6",
"protein_id": "ENSP00000406160.2",
"transcript_support_level": 1,
"aa_start": 453,
"aa_end": null,
"aa_length": 630,
"cds_start": 1358,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1461,
"cdna_end": null,
"cdna_length": 2050,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1247C>T",
"hgvs_p": "p.Pro416Leu",
"transcript": "ENST00000315506.11",
"protein_id": "ENSP00000319363.7",
"transcript_support_level": 1,
"aa_start": 416,
"aa_end": null,
"aa_length": 593,
"cds_start": 1247,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 1455,
"cdna_end": null,
"cdna_length": 2330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1358C>T",
"hgvs_p": "p.Pro453Leu",
"transcript": "ENST00000359962.9",
"protein_id": "ENSP00000353047.6",
"transcript_support_level": 5,
"aa_start": 453,
"aa_end": null,
"aa_length": 630,
"cds_start": 1358,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1566,
"cdna_end": null,
"cdna_length": 2436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1307C>T",
"hgvs_p": "p.Pro436Leu",
"transcript": "ENST00000428900.6",
"protein_id": "ENSP00000416781.2",
"transcript_support_level": 2,
"aa_start": 436,
"aa_end": null,
"aa_length": 613,
"cds_start": 1307,
"cds_end": null,
"cds_length": 1842,
"cdna_start": 1472,
"cdna_end": null,
"cdna_length": 2320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1286C>T",
"hgvs_p": "p.Pro429Leu",
"transcript": "NM_001438024.1",
"protein_id": "NP_001424953.1",
"transcript_support_level": null,
"aa_start": 429,
"aa_end": null,
"aa_length": 606,
"cds_start": 1286,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1444,
"cdna_end": null,
"cdna_length": 2315,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1286C>T",
"hgvs_p": "p.Pro429Leu",
"transcript": "ENST00000620095.4",
"protein_id": "ENSP00000478875.1",
"transcript_support_level": 5,
"aa_start": 429,
"aa_end": null,
"aa_length": 606,
"cds_start": 1286,
"cds_end": null,
"cds_length": 1821,
"cdna_start": 1494,
"cdna_end": null,
"cdna_length": 2364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1205C>T",
"hgvs_p": "p.Pro402Leu",
"transcript": "ENST00000409143.5",
"protein_id": "ENSP00000387293.1",
"transcript_support_level": 2,
"aa_start": 402,
"aa_end": null,
"aa_length": 579,
"cds_start": 1205,
"cds_end": null,
"cds_length": 1740,
"cdna_start": 1442,
"cdna_end": null,
"cdna_length": 2082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "c.1154C>T",
"hgvs_p": "p.Pro385Leu",
"transcript": "ENST00000396886.7",
"protein_id": "ENSP00000380095.3",
"transcript_support_level": 2,
"aa_start": 385,
"aa_end": null,
"aa_length": 562,
"cds_start": 1154,
"cds_end": null,
"cds_length": 1689,
"cdna_start": 1380,
"cdna_end": null,
"cdna_length": 2250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "n.*392C>T",
"hgvs_p": null,
"transcript": "ENST00000409818.7",
"protein_id": "ENSP00000386580.3",
"transcript_support_level": 5,
"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": 1760,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"hgvs_c": "n.*392C>T",
"hgvs_p": null,
"transcript": "ENST00000409818.7",
"protein_id": "ENSP00000386580.3",
"transcript_support_level": 5,
"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": 1760,
"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": "ENSG00000287133",
"gene_hgnc_id": null,
"hgvs_c": "n.118+10442G>A",
"hgvs_p": null,
"transcript": "ENST00000775820.1",
"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": 274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MPP4",
"gene_hgnc_id": 13680,
"dbsnp": "rs745508809",
"frequency_reference_population": 0.000020648333,
"hom_count_reference_population": 0,
"allele_count_reference_population": 33,
"gnomad_exomes_af": 0.0000179795,
"gnomad_genomes_af": 0.0000460211,
"gnomad_exomes_ac": 26,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8666330575942993,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9480000138282776,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.522,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7593,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.906,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.09,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999811622515729,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000409474.8",
"gene_symbol": "MPP4",
"hgnc_id": 13680,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1379C>T",
"hgvs_p": "p.Pro460Leu"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000775820.1",
"gene_symbol": "ENSG00000287133",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.118+10442G>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
}