17-63830911-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002805.6(PSMC5):c.655C>T(p.Leu219Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 1,613,114 control chromosomes in the GnomAD database, including 329,422 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002805.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMC5 | NM_002805.6 | c.655C>T | p.Leu219Leu | synonymous_variant | Exon 7 of 12 | ENST00000310144.11 | NP_002796.4 | |
PSMC5 | NM_001199163.2 | c.631C>T | p.Leu211Leu | synonymous_variant | Exon 7 of 12 | NP_001186092.1 | ||
PSMC5 | XM_047436423.1 | c.655C>T | p.Leu219Leu | synonymous_variant | Exon 7 of 8 | XP_047292379.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.700 AC: 106235AN: 151658Hom.: 38638 Cov.: 29
GnomAD3 exomes AF: 0.649 AC: 163060AN: 251334Hom.: 54100 AF XY: 0.647 AC XY: 87859AN XY: 135836
GnomAD4 exome AF: 0.627 AC: 916891AN: 1461338Hom.: 290724 Cov.: 65 AF XY: 0.629 AC XY: 457163AN XY: 726984
GnomAD4 genome AF: 0.701 AC: 106352AN: 151776Hom.: 38698 Cov.: 29 AF XY: 0.701 AC XY: 51972AN XY: 74126
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at