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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: 13-47954148-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=13&pos=47954148&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "13",
"pos": 47954148,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000646932.1",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "c.1099G>T",
"hgvs_p": "p.Asp367Tyr",
"transcript": "NM_003850.3",
"protein_id": "NP_003841.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 463,
"cds_start": 1099,
"cds_end": null,
"cds_length": 1392,
"cdna_start": 1103,
"cdna_end": null,
"cdna_length": 2111,
"mane_select": "ENST00000646932.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "c.1099G>T",
"hgvs_p": "p.Asp367Tyr",
"transcript": "ENST00000646932.1",
"protein_id": "ENSP00000494360.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 463,
"cds_start": 1099,
"cds_end": null,
"cds_length": 1392,
"cdna_start": 1103,
"cdna_end": null,
"cdna_length": 2111,
"mane_select": "NM_003850.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "c.1162G>T",
"hgvs_p": "p.Asp388Tyr",
"transcript": "ENST00000643023.1",
"protein_id": "ENSP00000495664.1",
"transcript_support_level": null,
"aa_start": 388,
"aa_end": null,
"aa_length": 484,
"cds_start": 1162,
"cds_end": null,
"cds_length": 1455,
"cdna_start": 1198,
"cdna_end": null,
"cdna_length": 2201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "c.925G>T",
"hgvs_p": "p.Asp309Tyr",
"transcript": "ENST00000642944.1",
"protein_id": "ENSP00000495674.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 405,
"cds_start": 925,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 1123,
"cdna_end": null,
"cdna_length": 2006,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "c.925G>T",
"hgvs_p": "p.Asp309Tyr",
"transcript": "ENST00000646804.1",
"protein_id": "ENSP00000493977.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 405,
"cds_start": 925,
"cds_end": null,
"cds_length": 1218,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 2321,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"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": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "c.889G>T",
"hgvs_p": "p.Asp297Tyr",
"transcript": "ENST00000434484.5",
"protein_id": "ENSP00000392771.1",
"transcript_support_level": 5,
"aa_start": 297,
"aa_end": null,
"aa_length": 297,
"cds_start": 889,
"cds_end": null,
"cds_length": 894,
"cdna_start": 889,
"cdna_end": null,
"cdna_length": 894,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "n.407G>T",
"hgvs_p": null,
"transcript": "ENST00000467222.1",
"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": 710,
"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": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "n.*298G>T",
"hgvs_p": null,
"transcript": "ENST00000634878.2",
"protein_id": "ENSP00000489542.1",
"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": 830,
"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": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "n.1099G>T",
"hgvs_p": null,
"transcript": "ENST00000643584.1",
"protein_id": "ENSP00000494987.1",
"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": 3317,
"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": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "n.*892G>T",
"hgvs_p": null,
"transcript": "ENST00000647361.1",
"protein_id": "ENSP00000494607.1",
"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": 2316,
"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": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "n.*298G>T",
"hgvs_p": null,
"transcript": "ENST00000634878.2",
"protein_id": "ENSP00000489542.1",
"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": 830,
"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": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"hgvs_c": "n.*892G>T",
"hgvs_p": null,
"transcript": "ENST00000647361.1",
"protein_id": "ENSP00000494607.1",
"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": 2316,
"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": "ENSG00000287456",
"gene_hgnc_id": null,
"hgvs_c": "n.59-1699C>A",
"hgvs_p": null,
"transcript": "ENST00000657958.1",
"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": 1042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SUCLA2",
"gene_hgnc_id": 11448,
"dbsnp": "rs117412559",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9572980403900146,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.912,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9705,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.41,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.512,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000646932.1",
"gene_symbol": "SUCLA2",
"hgnc_id": 11448,
"effects": [
"missense_variant"
],
"inheritance_mode": "Mitochondrial,AR",
"hgvs_c": "c.1099G>T",
"hgvs_p": "p.Asp367Tyr"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000657958.1",
"gene_symbol": "ENSG00000287456",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.59-1699C>A",
"hgvs_p": null
}
],
"clinvar_disease": " encephalomyopathic form with methylmalonic aciduria,Mitochondrial DNA depletion syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}