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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: 12-119850217-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=119850217&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 119850217,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000392521.7",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "NM_001206999.2",
"protein_id": "NP_001193928.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2069,
"cds_start": 473,
"cds_end": null,
"cds_length": 6210,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8736,
"mane_select": "ENST00000392521.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "ENST00000392521.7",
"protein_id": "ENSP00000376306.2",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 2069,
"cds_start": 473,
"cds_end": null,
"cds_length": 6210,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8736,
"mane_select": "NM_001206999.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "ENST00000261833.11",
"protein_id": "ENSP00000261833.7",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 2027,
"cds_start": 473,
"cds_end": null,
"cds_length": 6084,
"cdna_start": 526,
"cdna_end": null,
"cdna_length": 8578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "NM_007174.3",
"protein_id": "NP_009105.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2027,
"cds_start": 473,
"cds_end": null,
"cds_length": 6084,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.224C>G",
"hgvs_p": "p.Pro75Arg",
"transcript": "ENST00000536325.1",
"protein_id": "ENSP00000443199.1",
"transcript_support_level": 3,
"aa_start": 75,
"aa_end": null,
"aa_length": 108,
"cds_start": 224,
"cds_end": null,
"cds_length": 329,
"cdna_start": 224,
"cdna_end": null,
"cdna_length": 329,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_011537783.2",
"protein_id": "XP_011536085.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2084,
"cds_start": 473,
"cds_end": null,
"cds_length": 6255,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_011537784.2",
"protein_id": "XP_011536086.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2083,
"cds_start": 473,
"cds_end": null,
"cds_length": 6252,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8778,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_011537785.2",
"protein_id": "XP_011536087.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2069,
"cds_start": 473,
"cds_end": null,
"cds_length": 6210,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8736,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_017018735.2",
"protein_id": "XP_016874224.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2068,
"cds_start": 473,
"cds_end": null,
"cds_length": 6207,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_017018736.2",
"protein_id": "XP_016874225.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2068,
"cds_start": 473,
"cds_end": null,
"cds_length": 6207,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_006719206.3",
"protein_id": "XP_006719269.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2054,
"cds_start": 473,
"cds_end": null,
"cds_length": 6165,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_017018737.2",
"protein_id": "XP_016874226.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2053,
"cds_start": 473,
"cds_end": null,
"cds_length": 6162,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_047428134.1",
"protein_id": "XP_047284090.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2026,
"cds_start": 473,
"cds_end": null,
"cds_length": 6081,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_011537787.2",
"protein_id": "XP_011536089.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2012,
"cds_start": 473,
"cds_end": null,
"cds_length": 6039,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8565,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg",
"transcript": "XM_011537788.2",
"protein_id": "XP_011536090.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 2011,
"cds_start": 473,
"cds_end": null,
"cds_length": 6036,
"cdna_start": 558,
"cdna_end": null,
"cdna_length": 8562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CIT",
"gene_hgnc_id": 1985,
"dbsnp": "rs879255524",
"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": 0.8056281805038452,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.43,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9512,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.644,
"phylop100way_prediction": "Pathogenic",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000392521.7",
"gene_symbol": "CIT",
"hgnc_id": 1985,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.473C>G",
"hgvs_p": "p.Pro158Arg"
}
],
"clinvar_disease": "Autosomal recessive primary microcephaly",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Autosomal recessive primary microcephaly",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}