chrX-49274368-C-T

Variant names:

• chrX-49274368-C-T
• rs5906761
• NM_033215.5:c.1004+3495C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033215.5(PPP1R3F):​c.1004+3495C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.52 (11008 hom., 16771 hem., cov: 23)
  • Exomes 𝑓: 0.52 (2 hom. 18 hem.)
  • Failed GnomAD Quality Control
• Consequence: PPP1R3F NM_033215.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 9 publications found

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]

ENSG00000270012 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R3F	NM_033215.5	c.1004+3495C>T		intron_variant	Intron 1 of 3	ENST00000055335.11	NP_149992.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R3F	ENST00000055335.11	c.1004+3495C>T		intron_variant	Intron 1 of 3	2	NM_033215.5	ENSP00000055335.6

Frequencies

GnomAD3 genomes AF: 0.520 AC: 57646 AN: 110920 Hom.: 11005 Cov.: 23

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.584

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.528

GnomAD4 exome AF: 0.524 AC: 33 AN: 63 Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 18 AN XY: 27

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 1 AN: 1

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.381 AC: 8 AN: 21

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.579 AC: 22 AN: 38

Other (OTH) AF: 1.00 AC: 1 AN: 1

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.520 AC: 57684 AN: 110972 Hom.: 11008 Cov.: 23 AF XY: 0.505 AC XY: 16771 AN XY: 33220

African (AFR) AF: 0.434 AC: 13230 AN: 30474

American (AMR) AF: 0.457 AC: 4851 AN: 10623

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 1565 AN: 2629

East Asian (EAS) AF: 0.377 AC: 1311 AN: 3474

South Asian (SAS) AF: 0.574 AC: 1517 AN: 2641

European-Finnish (FIN) AF: 0.484 AC: 2889 AN: 5973

Middle Eastern (MID) AF: 0.580 AC: 123 AN: 212

European-Non Finnish (NFE) AF: 0.588 AC: 31036 AN: 52748

Other (OTH) AF: 0.532 AC: 808 AN: 1520

Alfa AF: 0.560 Hom.: 21564

Bravo AF: 0.512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.035
DANN	Benign	0.33
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5906761; hg19: chrX-49130831;