Variant 6-30602597-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The ENST00000376511.7(PPP1R10):c.2052C>T(p.Gly684=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00626 in 1,574,682 control chromosomes in the GnomAD database, including 269 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.024 ( 129 hom., cov: 32)

Exomes 𝑓: 0.0043 ( 140 hom. )

Consequence

PPP1R10
ENST00000376511.7 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.740

Variant links:

Genes affected

PPP1R10 (HGNC:9284): (protein phosphatase 1 regulatory subunit 10) This gene encodes a protein phosphatase 1 binding protein. The encoded protein plays a role in many cellular processes including cell cycle progression, DNA repair and apoptosis by regulating the activity of protein phosphatase 1. This gene lies within the major histocompatibility complex class I region on chromosome 6, and alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

PPP1R10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 6-30602597-G-A is Benign according to our data. Variant chr6-30602597-G-A is described in ClinVar as [Benign]. Clinvar id is 1276843.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.74 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.073 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
PPP1R10	NM_002714.4 linkuse as main transcript	c.2052C>T	p.Gly684=	synonymous_variant	19/20	ENST00000376511.7	NP_002705.2
PPP1R10	NM_001376195.1 linkuse as main transcript	c.2052C>T	p.Gly684=	synonymous_variant	19/20		NP_001363124.1
PPP1R10	XM_011514722.2 linkuse as main transcript	c.2052C>T	p.Gly684=	synonymous_variant	20/21		XP_011513024.1
PPP1R10	NR_072994.2 linkuse as main transcript	n.2543C>T		non_coding_transcript_exon_variant	19/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R10	ENST00000376511.7 linkuse as main transcript	c.2052C>T	p.Gly684=	synonymous_variant	19/20	1	NM_002714.4	ENSP00000365694	P1

Frequencies

GnomAD3 genomes

AF:

0.0243

AC:

3660

AN:

150674

Hom.:

129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0750

Gnomad AMI

AF:

0.00222

Gnomad AMR

AF:

0.0174

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.00198

Gnomad SAS

AF:

0.00356

Gnomad FIN

AF:

0.0000953

Gnomad MID

AF:

0.00331

Gnomad NFE

AF:

0.00276

Gnomad OTH

AF:

0.0275

GnomAD3 exomes

AF:

0.00827

AC:

1656

AN:

200140

Hom.:

AF XY:

0.00701

AC XY:

773

AN XY:

110320

show subpopulations

Gnomad AFR exome

AF:

0.0785

Gnomad AMR exome

AF:

0.00902

Gnomad ASJ exome

AF:

0.0157

Gnomad EAS exome

AF:

0.000698

Gnomad SAS exome

AF:

0.00275

Gnomad FIN exome

AF:

0.0000555

Gnomad NFE exome

AF:

0.00240

Gnomad OTH exome

AF:

0.00617

GnomAD4 exome

AF:

0.00434

AC:

6186

AN:

1423892

Hom.:

140

Cov.:

AF XY:

0.00410

AC XY:

2896

AN XY:

706016

show subpopulations

Gnomad4 AFR exome

AF:

0.0785

Gnomad4 AMR exome

AF:

0.00963

Gnomad4 ASJ exome

AF:

0.0173

Gnomad4 EAS exome

AF:

0.00132

Gnomad4 SAS exome

AF:

0.00318

Gnomad4 FIN exome

AF:

0.0000994

Gnomad4 NFE exome

AF:

0.00186

Gnomad4 OTH exome

AF:

0.00838

GnomAD4 genome

AF:

0.0244

AC:

3679

AN:

150790

Hom.:

129

Cov.:

AF XY:

0.0232

AC XY:

1706

AN XY:

73672

show subpopulations

Gnomad4 AFR

AF:

0.0752

Gnomad4 AMR

AF:

0.0173

Gnomad4 ASJ

AF:

0.0153

Gnomad4 EAS

AF:

0.00199

Gnomad4 SAS

AF:

0.00336

Gnomad4 FIN

AF:

0.0000953

Gnomad4 NFE

AF:

0.00276

Gnomad4 OTH

AF:

0.0272

Alfa

AF:

0.0122

Hom.:

Bravo

AF:

0.0266

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 16, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

5.6

DANN

Benign

0.66

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.9

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