dbSNP rs1569127888: PPP4R3C:p.Val692_Glu713del (chrX-27461156-GCTTCTCCTTCTTGGGTTCTTTTGGTCTCCATAAATTCATCGTCATCTTCCAGTGGTGGCATAACTA-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2

The NM_207319.4(PPP4R3C):c.2075_2140delTAGTTATGCCACCACTGGAAGATGACGATGAATTTATGGAGACCAAAAGAACCCAAGAAGGAGAAG(p.Val692_Glu713del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000996 in 401,577 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 22)

Exomes 𝑓: 0.000010 ( 0 hom. 4 hem. )

Consequence

PPP4R3C
NM_207319.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.00

Variant links:

Genes affected

PPP4R3C (HGNC:33146): (protein phosphatase 4 regulatory subunit 3C)

PPP4R3C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_207319.4.

BP6

Variant X-27461156-GCTTCTCCTTCTTGGGTTCTTTTGGTCTCCATAAATTCATCGTCATCTTCCAGTGGTGGCATAACTA-G is Benign according to our data. Variant chrX-27461156-GCTTCTCCTTCTTGGGTTCTTTTGGTCTCCATAAATTCATCGTCATCTTCCAGTGGTGGCATAACTA-G is described in ClinVar as [Likely_benign]. Clinvar id is 3771192.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP4R3C	NM_207319.4 link	c.2075_2140delTAGTTATGCCACCACTGGAAGATGACGATGAATTTATGGAGACCAAAAGAACCCAAGAAGGAGAAG	p.Val692_Glu713del	disruptive_inframe_deletion	Exon 1 of 1	ENST00000412172.4	NP_997202.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP4R3C	ENST00000412172.4 link	c.2075_2140delTAGTTATGCCACCACTGGAAGATGACGATGAATTTATGGAGACCAAAAGAACCCAAGAAGGAGAAG	p.Val692_Glu713del	disruptive_inframe_deletion	Exon 1 of 1	6	NM_207319.4	ENSP00000489770.1		Q6ZMV5-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000200

AC:

AN:

99861

Hom.:

AF XY:

0.0000539

AC XY:

AN XY:

37131

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000128

Gnomad SAS exome

AF:

0.0000713

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000996

AC:

AN:

401577

Hom.:

AF XY:

0.0000268

AC XY:

AN XY:

149021

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000415

Gnomad4 SAS exome

AF:

0.0000264

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000428

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Dec 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PPP4R3C: PM4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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