2-231062535-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002807.4(PSMD1):c.164G>A(p.Arg55Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000624 in 1,602,758 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_002807.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMD1 | NM_002807.4 | c.164G>A | p.Arg55Gln | missense_variant | Exon 4 of 25 | ENST00000308696.11 | NP_002798.2 | |
PSMD1 | NM_001191037.2 | c.164G>A | p.Arg55Gln | missense_variant | Exon 4 of 24 | NP_001177966.1 | ||
PSMD1 | XM_017004517.3 | c.164G>A | p.Arg55Gln | missense_variant | Exon 4 of 18 | XP_016860006.1 | ||
PSMD1 | NR_034059.2 | n.293+214G>A | intron_variant | Intron 3 of 23 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242048Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131268
GnomAD4 exome AF: 0.00000620 AC: 9AN: 1450592Hom.: 0 Cov.: 30 AF XY: 0.00000970 AC XY: 7AN XY: 721664
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.164G>A (p.R55Q) alteration is located in exon 4 (coding exon 4) of the PSMD1 gene. This alteration results from a G to A substitution at nucleotide position 164, causing the arginine (R) at amino acid position 55 to be replaced by a glutamine (Q). 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