rs2016457

Variant summary

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

The ENST00000322088.11(PPP2R1A):​c.808-148T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 648,794 control chromosomes in the GnomAD database, including 21,473 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 0.29 ( 6856 hom., cov: 32)
Exomes 𝑓: 0.23 ( 14617 hom. )

Consequence

PPP2R1A
ENST00000322088.11 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17
Variant links:
Genes affected
PPP2R1A (HGNC:9302): (protein phosphatase 2 scaffold subunit Aalpha) This gene encodes a constant regulatory subunit of protein phosphatase 2. Protein phosphatase 2 is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The constant regulatory subunit A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. This gene encodes an alpha isoform of the constant regulatory subunit A. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]

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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPP2R1ANM_014225.6 linkuse as main transcriptc.808-148T>A intron_variant ENST00000322088.11 NP_055040.2
PPP2R1ANM_001363656.2 linkuse as main transcriptc.271-148T>A intron_variant NP_001350585.1
PPP2R1ANR_033500.2 linkuse as main transcriptn.752-148T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPP2R1AENST00000322088.11 linkuse as main transcriptc.808-148T>A intron_variant 1 NM_014225.6 ENSP00000324804 P4

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
43704
AN:
151876
Hom.:
6839
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.416
Gnomad AMI
AF:
0.227
Gnomad AMR
AF:
0.217
Gnomad ASJ
AF:
0.285
Gnomad EAS
AF:
0.117
Gnomad SAS
AF:
0.136
Gnomad FIN
AF:
0.288
Gnomad MID
AF:
0.225
Gnomad NFE
AF:
0.251
Gnomad OTH
AF:
0.274
GnomAD4 exome
AF:
0.232
AC:
115350
AN:
496800
Hom.:
14617
AF XY:
0.228
AC XY:
59468
AN XY:
260602
show subpopulations
Gnomad4 AFR exome
AF:
0.423
Gnomad4 AMR exome
AF:
0.202
Gnomad4 ASJ exome
AF:
0.281
Gnomad4 EAS exome
AF:
0.0794
Gnomad4 SAS exome
AF:
0.143
Gnomad4 FIN exome
AF:
0.272
Gnomad4 NFE exome
AF:
0.247
Gnomad4 OTH exome
AF:
0.248
GnomAD4 genome
AF:
0.288
AC:
43779
AN:
151994
Hom.:
6856
Cov.:
32
AF XY:
0.285
AC XY:
21146
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.417
Gnomad4 AMR
AF:
0.217
Gnomad4 ASJ
AF:
0.285
Gnomad4 EAS
AF:
0.117
Gnomad4 SAS
AF:
0.136
Gnomad4 FIN
AF:
0.288
Gnomad4 NFE
AF:
0.251
Gnomad4 OTH
AF:
0.273
Alfa
AF:
0.272
Hom.:
730
Bravo
AF:
0.290
Asia WGS
AF:
0.163
AC:
569
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.22
DANN
Benign
0.50

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.

Other links and lift over

dbSNP: rs2016457; hg19: chr19-52718884; API