5-119489212-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_000414.4(HSD17B4):c.643C>T(p.Pro215Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,610,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000414.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD17B4 | NM_000414.4 | c.643C>T | p.Pro215Ser | missense_variant | Exon 9 of 24 | ENST00000510025.7 | NP_000405.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251122Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135714
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1458654Hom.: 0 Cov.: 29 AF XY: 0.0000193 AC XY: 14AN XY: 725844
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Pro240Ser variant in HSD17B4 has not been previously reported in individua ls with hearing loss, but has been identified in 3/16508 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSN P rs552078818). Although this variant has been seen in the general population, i ts frequency is not high enough to rule out a pathogenic role. Computational pre diction tools and conservation analysis do not provide strong support for or aga inst an impact to the protein. In summary, the clinical significance of the p.Pr o240Ser variant is uncertain. -
Bifunctional peroxisomal enzyme deficiency Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at