rs9262122

Variant names:

• chr6-30606065-T-C
• rs9262122
• NM_002714.4:c.741-30A>G

Variant summary

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

The NM_002714.4(PPP1R10):​c.741-30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,612,602 control chromosomes in the GnomAD database, including 18,548 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 (1390 hom., cov: 31)
  • Exomes 𝑓: 0.15 (17158 hom.)
• Consequence: PPP1R10 NM_002714.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 11 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002714.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R10	NM_002714.4	MANE Select	c.741-30A>G		intron	N/A	NP_002705.2
	PPP1R10	NM_001376195.1		c.741-30A>G		intron	N/A	NP_001363124.1
	PPP1R10	NR_072994.2		n.1293-30A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R10	ENST00000376511.7	TSL:1 MANE Select	c.741-30A>G		intron	N/A	ENSP00000365694.2
	PPP1R10	ENST00000461593.5	TSL:2	n.377-30A>G		intron	N/A
	PPP1R10	ENST00000468181.1	TSL:2	n.107-30A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17909 AN: 151916 Hom.: 1389 Cov.: 31

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0659

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.124

GnomAD2 exomes AF: 0.153 AC: 38512 AN: 251242 AF XY: 0.157

Gnomad AFR exome AF: 0.0242

Gnomad AMR exome AF: 0.204

Gnomad ASJ exome AF: 0.118

Gnomad EAS exome AF: 0.0531

Gnomad FIN exome AF: 0.169

Gnomad NFE exome AF: 0.159

Gnomad OTH exome AF: 0.152

GnomAD4 exome AF: 0.148 AC: 216495 AN: 1460568 Hom.: 17158 Cov.: 34 AF XY: 0.151 AC XY: 109544 AN XY: 726692

African (AFR) AF: 0.0216 AC: 723 AN: 33456

American (AMR) AF: 0.199 AC: 8916 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 3209 AN: 26126

East Asian (EAS) AF: 0.0567 AC: 2251 AN: 39692

South Asian (SAS) AF: 0.202 AC: 17389 AN: 86236

European-Finnish (FIN) AF: 0.169 AC: 9029 AN: 53418

Middle Eastern (MID) AF: 0.152 AC: 878 AN: 5766

European-Non Finnish (NFE) AF: 0.149 AC: 165596 AN: 1110804

Other (OTH) AF: 0.141 AC: 8504 AN: 60354

GnomAD4 genome AF: 0.118 AC: 17917 AN: 152034 Hom.: 1390 Cov.: 31 AF XY: 0.120 AC XY: 8903 AN XY: 74302

African (AFR) AF: 0.0294 AC: 1219 AN: 41512

American (AMR) AF: 0.156 AC: 2385 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3468

East Asian (EAS) AF: 0.0661 AC: 342 AN: 5176

South Asian (SAS) AF: 0.197 AC: 949 AN: 4808

European-Finnish (FIN) AF: 0.164 AC: 1733 AN: 10568

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10378 AN: 67944

Other (OTH) AF: 0.122 AC: 258 AN: 2108

Alfa AF: 0.136 Hom.: 4088

Bravo AF: 0.114

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.55
DANN	Benign	0.73
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs9262122; hg19: chr6-30573842; COSMIC: COSV64739130; COSMIC: COSV64739130;