chr2-238253139-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_022817.3(PER2):āc.2884T>Cā(p.Cys962Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,450,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022817.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.2884T>C | p.Cys962Arg | missense_variant | 19/23 | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.2884T>C | p.Cys962Arg | missense_variant | 19/23 | 1 | NM_022817.3 | P1 | |
ENST00000456601.1 | n.1525-1049A>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
PER2 | ENST00000707129.1 | c.2884T>C | p.Cys962Arg | missense_variant | 19/23 | P1 | |||
PER2 | ENST00000707130.1 | c.2884T>C | p.Cys962Arg | missense_variant | 19/23 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000811 AC: 2AN: 246616Hom.: 0 AF XY: 0.00000751 AC XY: 1AN XY: 133150
GnomAD4 exome AF: 0.00000414 AC: 6AN: 1450336Hom.: 0 Cov.: 34 AF XY: 0.00000556 AC XY: 4AN XY: 719252
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2023 | The c.2884T>C (p.C962R) alteration is located in exon 19 (coding exon 18) of the PER2 gene. This alteration results from a T to C substitution at nucleotide position 2884, causing the cysteine (C) at amino acid position 962 to be replaced by an arginine (R). 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