chr2-238253164-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_022817.3(PER2):c.2859C>T(p.Thr953=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000627 in 1,595,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
PER2
NM_022817.3 synonymous
NM_022817.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.534
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 2-238253164-G-A is Benign according to our data. Variant chr2-238253164-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 735943.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.534 with no splicing effect.
BS2
?
High AC in GnomAd at 60 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.2859C>T | p.Thr953= | synonymous_variant | 19/23 | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.2859C>T | p.Thr953= | synonymous_variant | 19/23 | 1 | NM_022817.3 | P1 | |
ENST00000456601.1 | n.1525-1024G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
PER2 | ENST00000707129.1 | c.2859C>T | p.Thr953= | synonymous_variant | 19/23 | P1 | |||
PER2 | ENST00000707130.1 | c.2859C>T | p.Thr953= | synonymous_variant | 19/23 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000394 AC: 60AN: 152220Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000913 AC: 22AN: 241052Hom.: 0 AF XY: 0.0000540 AC XY: 7AN XY: 129704
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GnomAD4 exome AF: 0.0000277 AC: 40AN: 1443294Hom.: 0 Cov.: 34 AF XY: 0.0000168 AC XY: 12AN XY: 714752
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at