rs2304672
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022817.3(PER2):c.-12C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.087 in 1,611,976 control chromosomes in the GnomAD database, including 6,907 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.093 ( 710 hom., cov: 33)
Exomes 𝑓: 0.086 ( 6197 hom. )
Consequence
PER2
NM_022817.3 5_prime_UTR
NM_022817.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.246
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.-12C>G | 5_prime_UTR_variant | 2/23 | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.-12C>G | 5_prime_UTR_variant | 2/23 | 1 | NM_022817.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0926 AC: 14092AN: 152172Hom.: 709 Cov.: 33
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GnomAD3 exomes AF: 0.0938 AC: 22785AN: 242956Hom.: 1294 AF XY: 0.0982 AC XY: 12939AN XY: 131782
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GnomAD4 exome AF: 0.0864 AC: 126151AN: 1459686Hom.: 6197 Cov.: 33 AF XY: 0.0892 AC XY: 64729AN XY: 726008
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GnomAD4 genome ? AF: 0.0926 AC: 14096AN: 152290Hom.: 710 Cov.: 33 AF XY: 0.0969 AC XY: 7215AN XY: 74460
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at