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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: 22-50526474-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=50526474&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 50526474,
"ref": "C",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000252029.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "NM_001953.5",
"protein_id": "NP_001944.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1050,
"cdna_end": null,
"cdna_length": 1586,
"mane_select": "ENST00000252029.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "ENST00000252029.8",
"protein_id": "ENSP00000252029.3",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1050,
"cdna_end": null,
"cdna_length": 1586,
"mane_select": "NM_001953.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "ENST00000395681.6",
"protein_id": "ENSP00000379038.1",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 487,
"cds_start": 931,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 1050,
"cdna_end": null,
"cdna_length": 1601,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "ENST00000395678.7",
"protein_id": "ENSP00000379036.3",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1082,
"cdna_end": null,
"cdna_length": 1614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "ENST00000395680.6",
"protein_id": "ENSP00000379037.1",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1085,
"cdna_end": null,
"cdna_length": 1621,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "ENST00000487577.5",
"protein_id": "ENSP00000498844.1",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1218,
"cdna_end": null,
"cdna_length": 1751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "NM_001257989.1",
"protein_id": "NP_001244918.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 487,
"cds_start": 931,
"cds_end": null,
"cds_length": 1464,
"cdna_start": 1123,
"cdna_end": null,
"cdna_length": 1674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "NM_001113755.3",
"protein_id": "NP_001107227.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1062,
"cdna_end": null,
"cdna_length": 1598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "NM_001113756.3",
"protein_id": "NP_001107228.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1234,
"cdna_end": null,
"cdna_length": 1770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys",
"transcript": "NM_001257988.1",
"protein_id": "NP_001244917.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 482,
"cds_start": 931,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 1158,
"cdna_end": null,
"cdna_length": 1694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.832G>T",
"hgvs_p": "p.Gly278Cys",
"transcript": "ENST00000425169.1",
"protein_id": "ENSP00000395875.1",
"transcript_support_level": 5,
"aa_start": 278,
"aa_end": null,
"aa_length": 444,
"cds_start": 832,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 929,
"cdna_end": null,
"cdna_length": 1432,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.812G>T",
"hgvs_p": "p.Gly271Val",
"transcript": "ENST00000650719.1",
"protein_id": "ENSP00000498276.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 324,
"cds_start": 812,
"cds_end": null,
"cds_length": 976,
"cdna_start": 937,
"cdna_end": null,
"cdna_length": 1101,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.430G>T",
"hgvs_p": "p.Gly144Cys",
"transcript": "ENST00000652401.1",
"protein_id": "ENSP00000498619.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 287,
"cds_start": 430,
"cds_end": null,
"cds_length": 864,
"cdna_start": 432,
"cdna_end": null,
"cdna_length": 866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.415G>T",
"hgvs_p": "p.Gly139Cys",
"transcript": "ENST00000651401.1",
"protein_id": "ENSP00000499115.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 168,
"cds_start": 415,
"cds_end": null,
"cds_length": 508,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 616,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "n.937G>T",
"hgvs_p": null,
"transcript": "ENST00000476284.1",
"protein_id": null,
"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": 1572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.-242G>T",
"hgvs_p": null,
"transcript": "NM_001169109.2",
"protein_id": "NP_001162580.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 266,
"cds_start": -4,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1054,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCO2",
"gene_hgnc_id": 10604,
"hgvs_c": "c.-242G>T",
"hgvs_p": null,
"transcript": "ENST00000543927.6",
"protein_id": "ENSP00000444433.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 266,
"cds_start": -4,
"cds_end": null,
"cds_length": 801,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "c.-138G>T",
"hgvs_p": null,
"transcript": "ENST00000651490.1",
"protein_id": "ENSP00000498433.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 79,
"cds_start": -4,
"cds_end": null,
"cds_length": 240,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 259,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"hgvs_c": "n.*417G>T",
"hgvs_p": null,
"transcript": "ENST00000652352.1",
"protein_id": "ENSP00000498579.1",
"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": 525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TYMP",
"gene_hgnc_id": 3148,
"dbsnp": "rs121913040",
"frequency_reference_population": 7.4679923e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.46799e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9066410660743713,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.781,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6662,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.44,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.264,
"phylop100way_prediction": "Benign",
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000252029.8",
"gene_symbol": "TYMP",
"hgnc_id": 3148,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.931G>T",
"hgvs_p": "p.Gly311Cys"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001169109.2",
"gene_symbol": "SCO2",
"hgnc_id": 10604,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-242G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Mitochondrial DNA depletion syndrome 1",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Mitochondrial DNA depletion syndrome 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}