Genetic Variant PPP1R10:c.2714-54G>A (chr6-30601712-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002714.4(PPP1R10):c.2714-54G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,482,492 control chromosomes in the GnomAD database, including 17,419 homozygotes. 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 0.12 ( 1398 hom., cov: 32)

Exomes 𝑓: 0.15 ( 16021 hom. )

Consequence

PPP1R10
NM_002714.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.538

Publications

15 publications found

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
PPP1R10	NM_002714.4 link	c.2714-54G>A	intron_variant	Intron 19 of 19	ENST00000376511.7	NP_002705.2
PPP1R10	NM_001376195.1 link	c.2714-54G>A	intron_variant	Intron 19 of 19		NP_001363124.1
PPP1R10	NR_072994.2 link	n.3205-54G>A	intron_variant	Intron 19 of 19
PPP1R10	XM_011514722.2 link	c.2714-54G>A	intron_variant	Intron 20 of 20		XP_011513024.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R10	ENST00000376511.7 link	c.2714-54G>A		intron_variant	Intron 19 of 19	1	NM_002714.4	ENSP00000365694.2

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17977

AN:

152032

Hom.:

1397

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0295

Gnomad AMI

AF:

0.217

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.0664

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.151

AC:

200927

AN:

1330342

Hom.:

16021

Cov.:

AF XY:

0.153

AC XY:

102196

AN XY:

665900

show subpopulations

African (AFR)

AF:

0.0226

AC:

695

AN:

30748

American (AMR)

AF:

0.201

AC:

8359

AN:

41588

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

3009

AN:

24260

East Asian (EAS)

AF:

0.0572

AC:

2202

AN:

38526

South Asian (SAS)

AF:

0.204

AC:

16605

AN:

81424

European-Finnish (FIN)

AF:

0.170

AC:

8617

AN:

50546

Middle Eastern (MID)

AF:

0.154

AC:

851

AN:

5540

European-Non Finnish (NFE)

AF:

0.152

AC:

152563

AN:

1001664

Other (OTH)

AF:

0.143

AC:

8026

AN:

56046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

8871

17743

26614

35486

44357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5160

10320

15480

20640

25800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.118

AC:

17985

AN:

152150

Hom.:

1398

Cov.:

AF XY:

0.120

AC XY:

8936

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0295

AC:

1225

AN:

41518

American (AMR)

AF:

0.156

AC:

2390

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

405

AN:

3472

East Asian (EAS)

AF:

0.0666

AC:

345

AN:

5184

South Asian (SAS)

AF:

0.197

AC:

949

AN:

4818

European-Finnish (FIN)

AF:

0.164

AC:

1732

AN:

10592

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.153

AC:

10430

AN:

67972

Other (OTH)

AF:

0.123

AC:

259

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

806

1611

2417

3222

4028

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

208

416

624

832

1040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.139

Hom.:

5821

Bravo

AF:

0.114

Asia WGS

AF:

0.120

AC:

416

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

8.0

(source)

DANN

Benign

0.77

PhyloP100

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over