rs2230681
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002813.7(PSMD9):c.50T>A(p.Val17Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V17A) has been classified as Likely benign.
Frequency
Consequence
NM_002813.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSMD9 | NM_002813.7 | c.50T>A | p.Val17Asp | missense_variant | 1/6 | ENST00000541212.6 | |
PSMD9 | NM_001261400.3 | c.50T>A | p.Val17Asp | missense_variant | 1/4 | ||
PSMD9 | NR_048555.3 | n.117T>A | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMD9 | ENST00000541212.6 | c.50T>A | p.Val17Asp | missense_variant | 1/6 | 1 | NM_002813.7 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 36
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1444668Hom.: 0 Cov.: 64 AF XY: 0.00 AC XY: 0AN XY: 717186
GnomAD4 genome ? Cov.: 36
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at