5-134197859-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_002715.4(PPP2CA):c.858-15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,612,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
PPP2CA
NM_002715.4 intron
NM_002715.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.866
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 Likely_benign. Variant got -6 ACMG points.
BP6
Variant 5-134197859-C-T is Benign according to our data. Variant chr5-134197859-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1673379.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP2CA | NM_002715.4 | c.858-15G>A | intron_variant | ENST00000481195.6 | NP_002706.1 | |||
PPP2CA | NM_001355019.2 | c.663-15G>A | intron_variant | NP_001341948.1 | ||||
PPP2CA | NR_149151.2 | n.1113-15G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP2CA | ENST00000481195.6 | c.858-15G>A | intron_variant | 1 | NM_002715.4 | ENSP00000418447.1 | ||||
ENSG00000272772 | ENST00000519718.2 | c.103-23837G>A | intron_variant | 5 | ENSP00000430774.2 | |||||
ENSG00000273345 | ENST00000703317.1 | n.*829-15G>A | intron_variant | ENSP00000515260.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
1
AN:
152052
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00000808 AC: 2AN: 247662Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134194
GnomAD3 exomes
AF:
AC:
2
AN:
247662
Hom.:
AF XY:
AC XY:
2
AN XY:
134194
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459988Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 726386
GnomAD4 exome
AF:
AC:
15
AN:
1459988
Hom.:
Cov.:
29
AF XY:
AC XY:
8
AN XY:
726386
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74250
GnomAD4 genome
AF:
AC:
1
AN:
152052
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74250
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 06, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -2
DS_AL_spliceai
Position offset: -15
Find out detailed SpliceAI scores and Pangolin per-transcript scores at