1-7809988-T-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001377275.1(PER3):āc.1338T>Cā(p.Ser446=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 1,613,778 control chromosomes in the GnomAD database, including 681,373 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: š 0.92 ( 64581 hom., cov: 32)
Exomes š: 0.92 ( 616792 hom. )
Consequence
PER3
NM_001377275.1 synonymous
NM_001377275.1 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.441
Genes affected
PER3 (HGNC:8847): (period circadian regulator 3) 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 have been linked to sleep disorders. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP7
Synonymous conserved (PhyloP=-0.441 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PER3 | NM_001377275.1 | c.1338T>C | p.Ser446= | synonymous_variant | 12/22 | ENST00000377532.8 | |
LOC124903833 | XR_007065450.1 | n.1689A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PER3 | ENST00000377532.8 | c.1338T>C | p.Ser446= | synonymous_variant | 12/22 | 1 | NM_001377275.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.918 AC: 139666AN: 152162Hom.: 64532 Cov.: 32
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GnomAD3 exomes AF: 0.880 AC: 221176AN: 251212Hom.: 99019 AF XY: 0.891 AC XY: 121057AN XY: 135792
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GnomAD4 exome AF: 0.917 AC: 1340096AN: 1461498Hom.: 616792 Cov.: 44 AF XY: 0.919 AC XY: 667917AN XY: 727098
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GnomAD4 genome AF: 0.918 AC: 139771AN: 152280Hom.: 64581 Cov.: 32 AF XY: 0.915 AC XY: 68136AN XY: 74456
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Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at