rs2304674
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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.449-72T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,497,376 control chromosomes in the GnomAD database, including 63,915 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 0.34 ( 9605 hom., cov: 33)
Exomes 𝑓: 0.28 ( 54310 hom. )
Consequence
PER2
NM_022817.3 intron
NM_022817.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.766
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=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER2 | NM_022817.3 | c.449-72T>C | intron_variant | ENST00000254657.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER2 | ENST00000254657.8 | c.449-72T>C | intron_variant | 1 | NM_022817.3 | P1 | |||
PER2 | ENST00000355768.6 | n.449-72T>C | intron_variant, non_coding_transcript_variant | 1 | |||||
PER2 | ENST00000707129.1 | c.449-72T>C | intron_variant | P1 | |||||
PER2 | ENST00000707130.1 | c.449-72T>C | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.341 AC: 51872AN: 151936Hom.: 9594 Cov.: 33
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GnomAD4 exome AF: 0.281 AC: 377460AN: 1345322Hom.: 54310 AF XY: 0.281 AC XY: 188898AN XY: 671880
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GnomAD4 genome ? AF: 0.341 AC: 51923AN: 152054Hom.: 9605 Cov.: 33 AF XY: 0.347 AC XY: 25772AN XY: 74312
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at