rs757019549
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002807.4(PSMD1):āc.554T>Cā(p.Met185Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000513 in 1,558,852 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.554T>C | p.Met185Thr | missense_variant | Exon 6 of 25 | ENST00000308696.11 | NP_002798.2 | |
PSMD1 | NM_001191037.2 | c.554T>C | p.Met185Thr | missense_variant | Exon 6 of 24 | NP_001177966.1 | ||
PSMD1 | XM_017004517.3 | c.554T>C | p.Met185Thr | missense_variant | Exon 6 of 18 | XP_016860006.1 | ||
PSMD1 | NR_034059.2 | n.543T>C | non_coding_transcript_exon_variant | Exon 5 of 24 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000137 AC: 3AN: 219178Hom.: 0 AF XY: 0.00000835 AC XY: 1AN XY: 119722
GnomAD4 exome AF: 0.00000427 AC: 6AN: 1406612Hom.: 0 Cov.: 29 AF XY: 0.00000286 AC XY: 2AN XY: 699542
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.554T>C (p.M185T) alteration is located in exon 6 (coding exon 6) of the PSMD1 gene. This alteration results from a T to C substitution at nucleotide position 554, causing the methionine (M) at amino acid position 185 to be replaced by a threonine (T). 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