rs9262122

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.106
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PPP1R10NM_002714.4 linkuse as main transcriptc.741-30A>G intron_variant ENST00000376511.7
PPP1R10NM_001376195.1 linkuse as main transcriptc.741-30A>G intron_variant
PPP1R10XM_011514722.2 linkuse as main transcriptc.741-30A>G intron_variant
PPP1R10NR_072994.2 linkuse as main transcriptn.1293-30A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PPP1R10ENST00000376511.7 linkuse as main transcriptc.741-30A>G intron_variant 1 NM_002714.4 P1
PPP1R10ENST00000461593.5 linkuse as main transcriptn.377-30A>G intron_variant, non_coding_transcript_variant 2
PPP1R10ENST00000468181.1 linkuse as main transcriptn.107-30A>G intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.118
AC:
17909
AN:
151916
Hom.:
1389
Cov.:
31
show subpopulations
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
GnomAD3 exomes
AF:
0.153
AC:
38512
AN:
251242
Hom.:
3412
AF XY:
0.157
AC XY:
21359
AN XY:
135782
show subpopulations
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 SAS exome
AF:
0.203
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
show subpopulations
Gnomad4 AFR exome
AF:
0.0216
Gnomad4 AMR exome
AF:
0.199
Gnomad4 ASJ exome
AF:
0.123
Gnomad4 EAS exome
AF:
0.0567
Gnomad4 SAS exome
AF:
0.202
Gnomad4 FIN exome
AF:
0.169
Gnomad4 NFE exome
AF:
0.149
Gnomad4 OTH exome
AF:
0.141
GnomAD4 genome
AF:
0.118
AC:
17917
AN:
152034
Hom.:
1390
Cov.:
31
AF XY:
0.120
AC XY:
8903
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.0294
Gnomad4 AMR
AF:
0.156
Gnomad4 ASJ
AF:
0.117
Gnomad4 EAS
AF:
0.0661
Gnomad4 SAS
AF:
0.197
Gnomad4 FIN
AF:
0.164
Gnomad4 NFE
AF:
0.153
Gnomad4 OTH
AF:
0.122
Alfa
AF:
0.144
Hom.:
1313
Bravo
AF:
0.114
Asia WGS
AF:
0.119
AC:
414
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
0.55
DANN
Benign
0.73

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9262122; hg19: chr6-30573842; COSMIC: COSV64739130; COSMIC: COSV64739130; API