rs778265488
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000414.4(HSD17B4):c.1858G>A(p.Gly620Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD17B4 | NM_000414.4 | c.1858G>A | p.Gly620Arg | missense_variant | Exon 22 of 24 | ENST00000510025.7 | NP_000405.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251252Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135796
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461274Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726952
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152012Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74226
ClinVar
Submissions by phenotype
Bifunctional peroxisomal enzyme deficiency Uncertain:1
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not specified Uncertain:1
Variant classified as Uncertain Significance - Favor Benign. The p.Gly645Arg var iant in HSD17B4 has not been previously reported in individuals with hearing los s, but has been identified in 1/11454 Latino chromosomes by the Exome Aggregatio n Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs778265488). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Glycine (Gly) at position 645 is not cons erved in mammals or evolutionarily distant species and 2 mammals (killer whale a nd dolphin) carry a arginine (Arg), supporting that this change may be tolerated . Additional computational prediction tools suggest that the p.Gly645Arg varian t may not impact the protein, though this information is not predictive enough t o rule out pathogenicity. In summary, while the clinical significance of the p.G ly645Arg variant is uncertain, these data suggest that it is more likely to be b enign. -
Bifunctional peroxisomal enzyme deficiency;C4551721:Perrault syndrome 1 Uncertain:1
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Bifunctional peroxisomal enzyme deficiency;C0685838:Perrault syndrome Uncertain:1
This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 620 of the HSD17B4 protein (p.Gly620Arg). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with HSD17B4-related conditions. ClinVar contains an entry for this variant (Variation ID: 505307). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt HSD17B4 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at