2-238250644-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_022817.3(PER2):c.3374A>G(p.Glu1125Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,613,194 control chromosomes in the GnomAD database, including 1 homozygotes. 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_022817.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.3374A>G | p.Glu1125Gly | missense_variant | 21/23 | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.3374A>G | p.Glu1125Gly | missense_variant | 21/23 | 1 | NM_022817.3 | P1 | |
ENST00000456601.1 | n.1524+3127T>C | intron_variant, non_coding_transcript_variant | 2 | ||||||
PER2 | ENST00000707129.1 | c.3374A>G | p.Glu1125Gly | missense_variant | 21/23 | P1 | |||
PER2 | ENST00000707130.1 | c.3374A>G | p.Glu1125Gly | missense_variant | 21/23 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251348Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135876
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1460932Hom.: 1 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726876
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.3374A>G (p.E1125G) alteration is located in exon 21 (coding exon 20) of the PER2 gene. This alteration results from a A to G substitution at nucleotide position 3374, causing the glutamic acid (E) at amino acid position 1125 to be replaced by a glycine (G). 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