2-231067019-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_002807.4(PSMD1):c.418C>T(p.Arg140*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,500 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 (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_002807.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMD1 | NM_002807.4 | c.418C>T | p.Arg140* | stop_gained | Exon 5 of 25 | ENST00000308696.11 | NP_002798.2 | |
PSMD1 | NM_001191037.2 | c.418C>T | p.Arg140* | stop_gained | Exon 5 of 24 | NP_001177966.1 | ||
PSMD1 | XM_017004517.3 | c.418C>T | p.Arg140* | stop_gained | Exon 5 of 18 | XP_016860006.1 | ||
PSMD1 | NR_034059.2 | n.407C>T | non_coding_transcript_exon_variant | Exon 4 of 24 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461500Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727056
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
ACMG codes:PM2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at