17-39986702-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002809.4(PSMD3):c.539G>A(p.Arg180His) variant causes a missense change. The variant allele was found at a frequency of 0.0000527 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251440Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135894
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461832Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727218
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.539G>A (p.R180H) alteration is located in exon 3 (coding exon 3) of the PSMD3 gene. This alteration results from a G to A substitution at nucleotide position 539, causing the arginine (R) at amino acid position 180 to be replaced by a histidine (H). 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