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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: 19-40394105-G-GACA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40394105&ref=G&alt=GACA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40394105,
"ref": "G",
"alt": "GACA",
"effect": "conservative_inframe_insertion",
"transcript": "ENST00000324001.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.4244_4246dupTGT",
"hgvs_p": "p.Val1415_Ser1416insLeu",
"transcript": "NM_181882.3",
"protein_id": "NP_870998.2",
"transcript_support_level": null,
"aa_start": 1416,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4246,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4529,
"cdna_end": null,
"cdna_length": 4867,
"mane_select": "ENST00000324001.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.4244_4246dupTGT",
"hgvs_p": "p.Val1415_Ser1416insLeu",
"transcript": "ENST00000324001.8",
"protein_id": "ENSP00000326018.6",
"transcript_support_level": 1,
"aa_start": 1416,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4246,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4529,
"cdna_end": null,
"cdna_length": 4867,
"mane_select": "NM_181882.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.*4449_*4451dupTGT",
"hgvs_p": null,
"transcript": "ENST00000291825.11",
"protein_id": "ENSP00000291825.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 147,
"cds_start": -4,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.4529_4531dupTGT",
"hgvs_p": "p.Val1510_Ser1511insLeu",
"transcript": "NM_001411127.1",
"protein_id": "NP_001398056.1",
"transcript_support_level": null,
"aa_start": 1511,
"aa_end": null,
"aa_length": 1556,
"cds_start": 4531,
"cds_end": null,
"cds_length": 4671,
"cdna_start": 4578,
"cdna_end": null,
"cdna_length": 4916,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.4529_4531dupTGT",
"hgvs_p": "p.Val1510_Ser1511insLeu",
"transcript": "ENST00000674005.2",
"protein_id": "ENSP00000501261.1",
"transcript_support_level": null,
"aa_start": 1511,
"aa_end": null,
"aa_length": 1556,
"cds_start": 4531,
"cds_end": null,
"cds_length": 4671,
"cdna_start": 4582,
"cdna_end": null,
"cdna_length": 4920,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.4103_4105dupTGT",
"hgvs_p": "p.Val1368_Ser1369insLeu",
"transcript": "ENST00000676076.1",
"protein_id": "ENSP00000502166.1",
"transcript_support_level": null,
"aa_start": 1369,
"aa_end": null,
"aa_length": 1414,
"cds_start": 4105,
"cds_end": null,
"cds_length": 4245,
"cdna_start": 4107,
"cdna_end": null,
"cdna_length": 4447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.3827_3829dupTGT",
"hgvs_p": "p.Val1276_Ser1277insLeu",
"transcript": "ENST00000673881.1",
"protein_id": "ENSP00000501070.1",
"transcript_support_level": null,
"aa_start": 1277,
"aa_end": null,
"aa_length": 1322,
"cds_start": 3829,
"cds_end": null,
"cds_length": 3969,
"cdna_start": 4645,
"cdna_end": null,
"cdna_length": 4985,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.3827_3829dupTGT",
"hgvs_p": "p.Val1276_Ser1277insLeu",
"transcript": "ENST00000674773.1",
"protein_id": "ENSP00000502579.1",
"transcript_support_level": null,
"aa_start": 1277,
"aa_end": null,
"aa_length": 1322,
"cds_start": 3829,
"cds_end": null,
"cds_length": 3969,
"cdna_start": 4095,
"cdna_end": null,
"cdna_length": 4433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "LS",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.4142_4144dupTGT",
"hgvs_p": "p.Val1381_Ser1382insLeu",
"transcript": "XM_017027047.2",
"protein_id": "XP_016882536.1",
"transcript_support_level": null,
"aa_start": 1382,
"aa_end": null,
"aa_length": 1427,
"cds_start": 4144,
"cds_end": null,
"cds_length": 4284,
"cdna_start": 4215,
"cdna_end": null,
"cdna_length": 4553,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "n.*3994_*3996dupTGT",
"hgvs_p": null,
"transcript": "ENST00000676260.1",
"protein_id": "ENSP00000502436.1",
"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": 4348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.*4449_*4451dupTGT",
"hgvs_p": null,
"transcript": "NM_020956.2",
"protein_id": "NP_066007.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 147,
"cds_start": -4,
"cds_end": null,
"cds_length": 444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.*3838_*3840dupTGT",
"hgvs_p": null,
"transcript": "ENST00000676316.1",
"protein_id": "ENSP00000501881.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 96,
"cds_start": -4,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "c.*3838_*3840dupTGT",
"hgvs_p": null,
"transcript": "ENST00000675517.1",
"protein_id": "ENSP00000501865.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 92,
"cds_start": -4,
"cds_end": null,
"cds_length": 279,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4261,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"hgvs_c": "n.*3994_*3996dupTGT",
"hgvs_p": null,
"transcript": "ENST00000676260.1",
"protein_id": "ENSP00000502436.1",
"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": 4348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRX",
"gene_hgnc_id": 13797,
"dbsnp": "rs771234852",
"frequency_reference_population": 0.0001292579,
"hom_count_reference_population": 1,
"allele_count_reference_population": 208,
"gnomad_exomes_af": 0.000133146,
"gnomad_genomes_af": 0.0000920193,
"gnomad_exomes_ac": 194,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": -0.131,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4_Supporting,BS1_Supporting",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 1,
"pathogenic_score": 1,
"criteria": [
"PM4_Supporting",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000324001.8",
"gene_symbol": "PRX",
"hgnc_id": 13797,
"effects": [
"conservative_inframe_insertion"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4244_4246dupTGT",
"hgvs_p": "p.Val1415_Ser1416insLeu"
}
],
"clinvar_disease": "Charcot-Marie-Tooth disease type 4,Inborn genetic diseases,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 B:1",
"phenotype_combined": "Charcot-Marie-Tooth disease type 4|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}