rs16838698

Variant names:

• chr4-6384312-A-C
• rs16838698
• ENST00000513943.5:n.515T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-6384312-A-C
• chr4-6384312-A-G
• chr4-6384312-A-T

Variant summary

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

The ENST00000513943.5(PPP2R2C):​n.515T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 985,158 control chromosomes in the GnomAD database, including 209,299 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 0.57 (27047 hom., cov: 34)
  • Exomes 𝑓: 0.66 (182252 hom.)
• Consequence: PPP2R2C ENST00000513943.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.83
• Publications: 5 publications found

Genes affected

PPP2R2C (HGNC:9306): (protein phosphatase 2 regulatory subunit Bgamma) The product of this gene belongs to the phosphatase 2 regulatory subunit B family. 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 B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes a gamma isoform of the regulatory subunit B55 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R2C	NM_020416.4	c.71-3218T>G		intron_variant	Intron 1 of 8	ENST00000382599.9	NP_065149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP2R2C	ENST00000382599.9	c.71-3218T>G		intron_variant	Intron 1 of 8	1	NM_020416.4	ENSP00000372042.4

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86633 AN: 152068 Hom.: 27039 Cov.: 34

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.584

GnomAD4 exome AF: 0.659 AC: 548803 AN: 832972 Hom.: 182252 Cov.: 34 AF XY: 0.659 AC XY: 253321 AN XY: 384660

African (AFR) AF: 0.250 AC: 3951 AN: 15782

American (AMR) AF: 0.708 AC: 697 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 3552 AN: 5150

East Asian (EAS) AF: 0.681 AC: 2469 AN: 3626

South Asian (SAS) AF: 0.584 AC: 9604 AN: 16452

European-Finnish (FIN) AF: 0.683 AC: 190 AN: 278

Middle Eastern (MID) AF: 0.601 AC: 974 AN: 1620

European-Non Finnish (NFE) AF: 0.669 AC: 509934 AN: 761784

Other (OTH) AF: 0.639 AC: 17432 AN: 27296

GnomAD4 genome AF: 0.569 AC: 86659 AN: 152186 Hom.: 27047 Cov.: 34 AF XY: 0.574 AC XY: 42749 AN XY: 74420

African (AFR) AF: 0.289 AC: 12015 AN: 41516

American (AMR) AF: 0.695 AC: 10631 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2442 AN: 3472

East Asian (EAS) AF: 0.689 AC: 3566 AN: 5176

South Asian (SAS) AF: 0.580 AC: 2794 AN: 4820

European-Finnish (FIN) AF: 0.702 AC: 7437 AN: 10598

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45702 AN: 67998

Other (OTH) AF: 0.580 AC: 1227 AN: 2114

Alfa AF: 0.620 Hom.: 59683

Bravo AF: 0.561

Asia WGS AF: 0.605 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		2.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16838698; hg19: chr4-6386039;