Variant rs8179074 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002666.5(PLIN1):c.1248C>T(p.Phe416=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 1,535,726 control chromosomes in the GnomAD database, including 2,198 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.040 ( 180 hom., cov: 32)

Exomes 𝑓: 0.051 ( 2018 hom. )

Consequence

PLIN1
NM_002666.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.16

Variant links:

Genes affected

PLIN1 (HGNC:9076): (perilipin 1) The protein encoded by this gene coats lipid storage droplets in adipocytes, thereby protecting them until they can be broken down by hormone-sensitive lipase. The encoded protein is the major cAMP-dependent protein kinase substrate in adipocytes and, when unphosphorylated, may play a role in the inhibition of lipolysis. Alternatively spliced transcript variants varying in the 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Feb 2009]

PLIN1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 15-89665904-G-A is Benign according to our data. Variant chr15-89665904-G-A is described in ClinVar as [Benign]. Clinvar id is 129972.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-89665904-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.16 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLIN1	NM_002666.5 linkuse as main transcript	c.1248C>T	p.Phe416=	synonymous_variant	9/9	ENST00000300055.10	NP_002657.3
PLIN1	NM_001145311.2 linkuse as main transcript	c.1248C>T	p.Phe416=	synonymous_variant	9/9		NP_001138783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
PLIN1	ENST00000300055.10 linkuse as main transcript	c.1248C>T	p.Phe416=	synonymous_variant	9/9	1	NM_002666.5	ENSP00000300055	P1
PLIN1	ENST00000430628.2 linkuse as main transcript	c.1248C>T	p.Phe416=	synonymous_variant	9/9	5		ENSP00000402167	P1
PLIN1	ENST00000560330.1 linkuse as main transcript	c.124-963C>T		intron_variant		5		ENSP00000453426

Frequencies

GnomAD3 genomes

AF:

0.0400

AC:

6077

AN:

152088

Hom.:

180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00958

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0350

Gnomad ASJ

AF:

0.0628

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0149

Gnomad FIN

AF:

0.0558

Gnomad MID

AF:

0.0350

Gnomad NFE

AF:

0.0593

Gnomad OTH

AF:

0.0473

GnomAD3 exomes

AF:

0.0387

AC:

5975

AN:

154556

Hom.:

164

AF XY:

0.0394

AC XY:

3431

AN XY:

87124

show subpopulations

Gnomad AFR exome

AF:

0.00782

Gnomad AMR exome

AF:

0.0285

Gnomad ASJ exome

AF:

0.0593

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0181

Gnomad FIN exome

AF:

0.0495

Gnomad NFE exome

AF:

0.0530

Gnomad OTH exome

AF:

0.0574

GnomAD4 exome

AF:

0.0506

AC:

70041

AN:

1383524

Hom.:

2018

Cov.:

AF XY:

0.0500

AC XY:

34281

AN XY:

685416

show subpopulations

Gnomad4 AFR exome

AF:

0.00807

Gnomad4 AMR exome

AF:

0.0316

Gnomad4 ASJ exome

AF:

0.0628

Gnomad4 EAS exome

AF:

0.000176

Gnomad4 SAS exome

AF:

0.0181

Gnomad4 FIN exome

AF:

0.0566

Gnomad4 NFE exome

AF:

0.0561

Gnomad4 OTH exome

AF:

0.0481

GnomAD4 genome

AF:

0.0399

AC:

6075

AN:

152202

Hom.:

180

Cov.:

AF XY:

0.0394

AC XY:

2932

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.00955

Gnomad4 AMR

AF:

0.0348

Gnomad4 ASJ

AF:

0.0628

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.0151

Gnomad4 FIN

AF:

0.0558

Gnomad4 NFE

AF:

0.0593

Gnomad4 OTH

AF:

0.0473

Alfa

AF:

0.0493

Hom.:

Bravo

AF:

0.0379

Asia WGS

AF:

0.00808

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Mar 05, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.94

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over