Variant rs3027178 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002616.3(PER1):c.639A>C(p.Thr213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,612,592 control chromosomes in the GnomAD database, including 70,256 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 0.29 ( 6477 hom., cov: 32)

Exomes 𝑓: 0.29 ( 63779 hom. )

Consequence

PER1
NM_002616.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.13

Variant links:

Genes affected

PER1 (HGNC:8845): (period circadian regulator 1) 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. Alternative splicing has been observed in this gene; however, these variants have not been fully described. [provided by RefSeq, Jan 2014]

PER1 links:

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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=-0.91).

BP7

Synonymous conserved (PhyloP=-5.13 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PER1	NM_002616.3 linkuse as main transcript	c.639A>C	p.Thr213=	synonymous_variant	5/23	ENST00000317276.9	NP_002607.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PER1	ENST00000317276.9 linkuse as main transcript	c.639A>C	p.Thr213=	synonymous_variant	5/23	1	NM_002616.3	ENSP00000314420	P1	O15534-1

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43729

AN:

151934

Hom.:

6467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.413

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.287

GnomAD3 exomes

AF:

0.303

AC:

75731

AN:

250034

Hom.:

12664

AF XY:

0.295

AC XY:

39836

AN XY:

135158

show subpopulations

Gnomad AFR exome

AF:

0.257

Gnomad AMR exome

AF:

0.505

Gnomad ASJ exome

AF:

0.329

Gnomad EAS exome

AF:

0.274

Gnomad SAS exome

AF:

0.206

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.288

Gnomad OTH exome

AF:

0.308

GnomAD4 exome

AF:

0.291

AC:

425263

AN:

1460540

Hom.:

63779

Cov.:

AF XY:

0.288

AC XY:

209561

AN XY:

726578

show subpopulations

Gnomad4 AFR exome

AF:

0.253

Gnomad4 AMR exome

AF:

0.496

Gnomad4 ASJ exome

AF:

0.332

Gnomad4 EAS exome

AF:

0.304

Gnomad4 SAS exome

AF:

0.210

Gnomad4 FIN exome

AF:

0.232

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.289

GnomAD4 genome

AF:

0.288

AC:

43765

AN:

152052

Hom.:

6477

Cov.:

AF XY:

0.286

AC XY:

21283

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.255

Gnomad4 AMR

AF:

0.413

Gnomad4 ASJ

AF:

0.328

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.228

Gnomad4 NFE

AF:

0.293

Gnomad4 OTH

AF:

0.290

Alfa

AF:

0.292

Hom.:

2384

Bravo

AF:

0.304

Asia WGS

AF:

0.245

AC:

851

AN:

3478

EpiCase

AF:

0.307

EpiControl

AF:

0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.045

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over