Variant X-49270193-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_033215.5(PPP1R3F):c.324C>T(p.Pro108=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 1,093,993 control chromosomes in the GnomAD database, including 3,120 homozygotes. There are 28,042 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 223 hom., 2048 hem., cov: 24)

Exomes 𝑓: 0.086 ( 2897 hom. 25994 hem. )

Consequence

PPP1R3F
NM_033215.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.31

Variant links:

Genes affected

PPP1R3F (HGNC:14944): (protein phosphatase 1 regulatory subunit 3F) This gene encodes a protein that has been identified as one of several type-1 protein phosphatase (PP1) regulatory subunits. One or two of these subunits, together with the well-conserved catalytic subunit, can form the PP1 holoenzyme, where the regulatory subunit functions to regulate substrate specificity and/or targeting to a particular cellular compartment. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

PPP1R3F links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant X-49270193-C-T is Benign according to our data. Variant chrX-49270193-C-T is described in ClinVar as [Benign]. Clinvar id is 1239227.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.31 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.09 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R3F	NM_033215.5 linkuse as main transcript	c.324C>T	p.Pro108=	synonymous_variant	1/4	ENST00000055335.11	NP_149992.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R3F	ENST00000055335.11 linkuse as main transcript	c.324C>T	p.Pro108=	synonymous_variant	1/4	2	NM_033215.5	ENSP00000055335	P1	Q6ZSY5-1
	ENST00000651462.1 linkuse as main transcript	n.310+19G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0604

AC:

6815

AN:

112775

Hom.:

223

Cov.:

AF XY:

0.0585

AC XY:

2046

AN XY:

34995

show subpopulations

Gnomad AFR

AF:

0.0133

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.0348

Gnomad ASJ

AF:

0.0465

Gnomad EAS

AF:

0.000281

Gnomad SAS

AF:

0.0112

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.00844

Gnomad NFE

AF:

0.0921

Gnomad OTH

AF:

0.0444

GnomAD3 exomes

AF:

0.0603

AC:

2917

AN:

48408

Hom.:

130

AF XY:

0.0509

AC XY:

378

AN XY:

7424

show subpopulations

Gnomad AFR exome

AF:

0.0153

Gnomad AMR exome

AF:

0.0196

Gnomad ASJ exome

AF:

0.0469

Gnomad EAS exome

AF:

0.000430

Gnomad SAS exome

AF:

0.0130

Gnomad FIN exome

AF:

0.120

Gnomad NFE exome

AF:

0.0901

Gnomad OTH exome

AF:

0.0685

GnomAD4 exome

AF:

0.0862

AC:

84579

AN:

981172

Hom.:

2897

Cov.:

AF XY:

0.0840

AC XY:

25994

AN XY:

309628

show subpopulations

Gnomad4 AFR exome

AF:

0.00895

Gnomad4 AMR exome

AF:

0.0218

Gnomad4 ASJ exome

AF:

0.0511

Gnomad4 EAS exome

AF:

0.000285

Gnomad4 SAS exome

AF:

0.0158

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.0957

Gnomad4 OTH exome

AF:

0.0691

GnomAD4 genome

AF:

0.0604

AC:

6817

AN:

112821

Hom.:

223

Cov.:

AF XY:

0.0584

AC XY:

2048

AN XY:

35051

show subpopulations

Gnomad4 AFR

AF:

0.0133

Gnomad4 AMR

AF:

0.0347

Gnomad4 ASJ

AF:

0.0465

Gnomad4 EAS

AF:

0.000282

Gnomad4 SAS

AF:

0.0120

Gnomad4 FIN

AF:

0.136

Gnomad4 NFE

AF:

0.0921

Gnomad4 OTH

AF:

0.0439

Alfa

AF:

0.0731

Hom.:

602

Bravo

AF:

0.0509

ClinVar

Significance: Benign

Submissions summary: Benign:2

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 10, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

9.1

DANN

Benign

0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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