ClinVar Miner

Submissions for variant NM_000414.4(HSD17B4):c.2060C>T (p.Thr687Ile)

gnomAD frequency: 0.00265  dbSNP: rs28943592
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000218324 SCV000269162 benign not specified 2014-11-24 criteria provided, single submitter clinical testing Thr712Ile in exon 24 of HSD17B4: This variant is not expected to have clinical s ignificance because it has been identified in 6.5% (13/200) of Han Chinese chrom osomes from a broad population by the 1000 Genomes Project (http://www.ncbi.nlm. nih.gov/projects/SNP; dbSNP rs28943592).
Illumina Laboratory Services, Illumina RCV000301707 SCV000452149 benign Perrault syndrome 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Laboratory Services, Illumina RCV000361158 SCV000452150 benign Bifunctional peroxisomal enzyme deficiency 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000218324 SCV000729945 benign not specified 2017-09-20 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000218324 SCV000917531 benign not specified 2018-02-01 criteria provided, single submitter clinical testing Variant summary: HSD17B4 c.2060C>T (p.Thr687Ile) results in a non-conservative amino acid change located in the SCP2 sterol-binding domain of in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0065 in 276846 control chromosomes, predominantly at a frequency of 0.08 within the East Asian subpopulation in the gnomAD database, including 57 homozygotes. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 27.045 fold of the estimated maximal expected allele frequency for a pathogenic variant in HSD17B4 causing D-Bifunctional Protein Deficiency phenotype (0.003), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. Multiple clinical diagnostic laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV001079319 SCV001113767 benign Bifunctional peroxisomal enzyme deficiency; Perrault syndrome 2024-01-31 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000966445 SCV001144223 benign not provided 2018-12-11 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002494555 SCV002800628 benign Bifunctional peroxisomal enzyme deficiency; Perrault syndrome 1 2022-02-23 criteria provided, single submitter clinical testing

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