chr2-238277924-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_022817.3(PER2):c.13G>T(p.Ala5Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000416 in 1,613,676 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A5G) has been classified as Uncertain significance.
Frequency
Consequence
NM_022817.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.13G>T | p.Ala5Ser | missense_variant | 2/23 | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.13G>T | p.Ala5Ser | missense_variant | 2/23 | 1 | NM_022817.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00193 AC: 294AN: 152252Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000696 AC: 172AN: 247300Hom.: 1 AF XY: 0.000425 AC XY: 57AN XY: 133984
GnomAD4 exome AF: 0.000258 AC: 377AN: 1461306Hom.: 2 Cov.: 33 AF XY: 0.000226 AC XY: 164AN XY: 726896
GnomAD4 genome AF: 0.00193 AC: 294AN: 152370Hom.: 2 Cov.: 32 AF XY: 0.00164 AC XY: 122AN XY: 74516
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at