1-7827188-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001377275.1(PER3):c.2259G>A(p.Pro753Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 1,610,900 control chromosomes in the GnomAD database, including 127,151 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001377275.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PER3 | NM_001377275.1 | c.2259G>A | p.Pro753Pro | synonymous_variant | Exon 18 of 22 | ENST00000377532.8 | NP_001364204.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.425 AC: 64596AN: 151852Hom.: 14662 Cov.: 32
GnomAD3 exomes AF: 0.430 AC: 105731AN: 245866Hom.: 25188 AF XY: 0.416 AC XY: 55698AN XY: 133738
GnomAD4 exome AF: 0.384 AC: 560026AN: 1458930Hom.: 112481 Cov.: 44 AF XY: 0.380 AC XY: 275859AN XY: 725436
GnomAD4 genome AF: 0.425 AC: 64652AN: 151970Hom.: 14670 Cov.: 32 AF XY: 0.424 AC XY: 31477AN XY: 74270
ClinVar
Submissions by phenotype
PER3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at