rs752077601
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002807.4(PSMD1):āc.485T>Cā(p.Val162Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000828 in 1,607,166 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 (ā ).
Frequency
Consequence
NM_002807.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMD1 | NM_002807.4 | c.485T>C | p.Val162Ala | missense_variant | Exon 5 of 25 | ENST00000308696.11 | NP_002798.2 | |
PSMD1 | NM_001191037.2 | c.485T>C | p.Val162Ala | missense_variant | Exon 5 of 24 | NP_001177966.1 | ||
PSMD1 | XM_017004517.3 | c.485T>C | p.Val162Ala | missense_variant | Exon 5 of 18 | XP_016860006.1 | ||
PSMD1 | NR_034059.2 | n.474T>C | non_coding_transcript_exon_variant | Exon 4 of 24 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000289 AC: 7AN: 242182Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 131098
GnomAD4 exome AF: 0.0000880 AC: 128AN: 1454948Hom.: 0 Cov.: 30 AF XY: 0.0000898 AC XY: 65AN XY: 723760
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.485T>C (p.V162A) alteration is located in exon 5 (coding exon 5) of the PSMD1 gene. This alteration results from a T to C substitution at nucleotide position 485, causing the valine (V) at amino acid position 162 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at