rs3895755

Variant summary

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

The NM_002715.4(PPP2CA):​c.102+112T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 886,418 control chromosomes in the GnomAD database, including 3,189 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 0.099 ( 880 hom., cov: 32)
Exomes 𝑓: 0.070 ( 2309 hom. )

Consequence

PPP2CA
NM_002715.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.273
Variant links:
Genes affected
PPP2CA (HGNC:9299): (protein phosphatase 2 catalytic subunit alpha) This gene encodes the phosphatase 2A catalytic subunit. Protein phosphatase 2A 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. This gene encodes an alpha isoform of the catalytic subunit. [provided by RefSeq, Jul 2008]

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=-0.82).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PPP2CANM_002715.4 linkuse as main transcriptc.102+112T>C intron_variant ENST00000481195.6 NP_002706.1 P67775-1B3KUN1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPP2CAENST00000481195.6 linkuse as main transcriptc.102+112T>C intron_variant 1 NM_002715.4 ENSP00000418447.1 P67775-1
ENSG00000272772ENST00000519718.2 linkuse as main transcriptc.102+112T>C intron_variant 5 ENSP00000430774.2 E5RI56
ENSG00000273345ENST00000703317.1 linkuse as main transcriptn.*73+17244T>C intron_variant ENSP00000515260.1 A0A8V8TQA6

Frequencies

GnomAD3 genomes
AF:
0.0991
AC:
14989
AN:
151244
Hom.:
873
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.130
Gnomad AMI
AF:
0.0319
Gnomad AMR
AF:
0.155
Gnomad ASJ
AF:
0.0836
Gnomad EAS
AF:
0.0552
Gnomad SAS
AF:
0.0988
Gnomad FIN
AF:
0.142
Gnomad MID
AF:
0.132
Gnomad NFE
AF:
0.0655
Gnomad OTH
AF:
0.120
GnomAD4 exome
AF:
0.0701
AC:
51522
AN:
735054
Hom.:
2309
Cov.:
10
AF XY:
0.0712
AC XY:
26512
AN XY:
372502
show subpopulations
Gnomad4 AFR exome
AF:
0.140
Gnomad4 AMR exome
AF:
0.175
Gnomad4 ASJ exome
AF:
0.0721
Gnomad4 EAS exome
AF:
0.0498
Gnomad4 SAS exome
AF:
0.109
Gnomad4 FIN exome
AF:
0.129
Gnomad4 NFE exome
AF:
0.0588
Gnomad4 OTH exome
AF:
0.0811
GnomAD4 genome
AF:
0.0992
AC:
15012
AN:
151364
Hom.:
880
Cov.:
32
AF XY:
0.105
AC XY:
7760
AN XY:
73994
show subpopulations
Gnomad4 AFR
AF:
0.130
Gnomad4 AMR
AF:
0.156
Gnomad4 ASJ
AF:
0.0836
Gnomad4 EAS
AF:
0.0547
Gnomad4 SAS
AF:
0.0990
Gnomad4 FIN
AF:
0.142
Gnomad4 NFE
AF:
0.0655
Gnomad4 OTH
AF:
0.121
Alfa
AF:
0.0383
Hom.:
30
Bravo
AF:
0.102
Asia WGS
AF:
0.0980
AC:
341
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
11
DANN
Benign
0.47
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs3895755; hg19: chr5-133561339; API