chr17-39986630-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002809.4(PSMD3):c.467C>T(p.Ser156Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002809.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSMD3 | ENST00000264639.9 | c.467C>T | p.Ser156Leu | missense_variant | Exon 3 of 12 | 1 | NM_002809.4 | ENSP00000264639.4 | ||
PSMD3 | ENST00000540504.2 | c.20C>T | p.Ser7Leu | missense_variant | Exon 1 of 4 | 3 | ENSP00000444980.2 | |||
PSMD3 | ENST00000415039.7 | n.202C>T | non_coding_transcript_exon_variant | Exon 3 of 13 | 2 | ENSP00000407410.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251486Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135918
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461872Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727238
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.467C>T (p.S156L) alteration is located in exon 3 (coding exon 3) of the PSMD3 gene. This alteration results from a C to T substitution at nucleotide position 467, causing the serine (S) at amino acid position 156 to be replaced by a leucine (L). 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