rs2304670
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_022817.3(PER2):c.1992G>A(p.Ala664=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 1,613,452 control chromosomes in the GnomAD database, including 7,586 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.098 ( 776 hom., cov: 33)
Exomes 𝑓: 0.091 ( 6810 hom. )
Consequence
PER2
NM_022817.3 synonymous
NM_022817.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.216
Genes affected
PER2 (HGNC:8846): (period circadian regulator 2) This gene is a member of the Period family of genes and is expressed in a circadian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in the mammalian brain. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene may increase the risk of getting certain cancers and have been linked to sleep disorders. [provided by RefSeq, Jan 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
Variant 2-238256995-C-T is Benign according to our data. Variant chr2-238256995-C-T is described in ClinVar as [Benign]. Clinvar id is 3055371.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.216 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.1992G>A | p.Ala664= | synonymous_variant | 17/23 | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.1992G>A | p.Ala664= | synonymous_variant | 17/23 | 1 | NM_022817.3 | P1 | |
PER2 | ENST00000707129.1 | c.1992G>A | p.Ala664= | synonymous_variant | 17/23 | P1 | |||
PER2 | ENST00000707130.1 | c.1992G>A | p.Ala664= | synonymous_variant | 17/23 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0977 AC: 14860AN: 152152Hom.: 776 Cov.: 33
GnomAD3 genomes
AF:
AC:
14860
AN:
152152
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0974 AC: 24462AN: 251084Hom.: 1437 AF XY: 0.102 AC XY: 13805AN XY: 135746
GnomAD3 exomes
AF:
AC:
24462
AN:
251084
Hom.:
AF XY:
AC XY:
13805
AN XY:
135746
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0914 AC: 133524AN: 1461182Hom.: 6810 Cov.: 32 AF XY: 0.0940 AC XY: 68339AN XY: 726928
GnomAD4 exome
AF:
AC:
133524
AN:
1461182
Hom.:
Cov.:
32
AF XY:
AC XY:
68339
AN XY:
726928
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0976 AC: 14868AN: 152270Hom.: 776 Cov.: 33 AF XY: 0.102 AC XY: 7600AN XY: 74440
GnomAD4 genome
AF:
AC:
14868
AN:
152270
Hom.:
Cov.:
33
AF XY:
AC XY:
7600
AN XY:
74440
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
264
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PER2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 11, 2019 | 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:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at