12-121899718-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002813.7(PSMD9):c.326C>T(p.Ala109Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,014 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_002813.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMD9 | NM_002813.7 | c.326C>T | p.Ala109Val | missense_variant | Exon 3 of 6 | ENST00000541212.6 | NP_002804.2 | |
PSMD9 | NM_001261400.3 | c.139-3288C>T | intron_variant | Intron 1 of 3 | NP_001248329.1 | |||
PSMD9 | NR_048555.3 | n.309-3288C>T | intron_variant | Intron 2 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSMD9 | ENST00000541212.6 | c.326C>T | p.Ala109Val | missense_variant | Exon 3 of 6 | 1 | NM_002813.7 | ENSP00000440485.1 | ||
ENSG00000256950 | ENST00000546333.1 | n.242-3288C>T | intron_variant | Intron 2 of 3 | 5 | ENSP00000477146.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250832Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135680
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461810Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727202
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.326C>T (p.A109V) alteration is located in exon 3 (coding exon 3) of the PSMD9 gene. This alteration results from a C to T substitution at nucleotide position 326, causing the alanine (A) at amino acid position 109 to be replaced by a valine (V). 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