rs4824747

chrX-49272561-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033215.5(PPP1R3F):c.1004+1688G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 112,524 control chromosomes in the GnomAD database, including 517 homozygotes. There are 3,413 hemizygotes in GnomAD. 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 0.099 (517 hom., 3413 hem., cov: 24)
• Consequence: PPP1R3F NM_033215.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP1R3F	NM_033215.5	c.1004+1688G>T		intron_variant		ENST00000055335.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP1R3F	ENST00000055335.11	c.1004+1688G>T		intron_variant		2	NM_033215.5	P1

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 11180 AN: 112473 Hom.: 513 Cov.: 24 AF XY: 0.0984 AC XY: 3409 AN XY: 34627

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.0349

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.0717

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0902

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0995 AC: 11191 AN: 112524 Hom.: 517 Cov.: 24 AF XY: 0.0984 AC XY: 3413 AN XY: 34688

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.0894

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.0976

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.124 Hom.: 2574

Bravo AF: 0.0954

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	2.6
Dann	Benign	0.82

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

Other links and lift over

dbSNP: rs4824747; hg19: chrX-49129023;