2-231062637-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002807.4(PSMD1):āc.266A>Gā(p.Asn89Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000246 in 1,612,078 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMD1 | NM_002807.4 | c.266A>G | p.Asn89Ser | missense_variant | Exon 4 of 25 | ENST00000308696.11 | NP_002798.2 | |
PSMD1 | NM_001191037.2 | c.266A>G | p.Asn89Ser | missense_variant | Exon 4 of 24 | NP_001177966.1 | ||
PSMD1 | XM_017004517.3 | c.266A>G | p.Asn89Ser | missense_variant | Exon 4 of 18 | XP_016860006.1 | ||
PSMD1 | NR_034059.2 | n.293+316A>G | intron_variant | Intron 3 of 23 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249726Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135126
GnomAD4 exome AF: 0.000264 AC: 386AN: 1459862Hom.: 0 Cov.: 30 AF XY: 0.000234 AC XY: 170AN XY: 726374
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.266A>G (p.N89S) alteration is located in exon 4 (coding exon 4) of the PSMD1 gene. This alteration results from a A to G substitution at nucleotide position 266, causing the asparagine (N) at amino acid position 89 to be replaced by a serine (S). 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