rs17055106

Variant names:

• chr8-26300332-G-A
• rs17055106
• NM_002717.4:c.82+6592G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-26300332-G-A
• chr8-26300332-G-C
• chr8-26300332-G-T

Variant summary

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

The NM_002717.4(PPP2R2A):​c.82+6592G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,968 control chromosomes in the GnomAD database, including 22,577 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 0.54 (22577 hom., cov: 32)
• Consequence: PPP2R2A NM_002717.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 0 publications found

Genes affected

PPP2R2A (HGNC:9304): (protein phosphatase 2 regulatory subunit Balpha) 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 an alpha isoform of the regulatory subunit B55 subfamily. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP2R2A	NM_002717.4	c.82+6592G>A		intron_variant	Intron 2 of 9	ENST00000380737.8	NP_002708.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP2R2A	ENST00000380737.8	c.82+6592G>A		intron_variant	Intron 2 of 9	1	NM_002717.4	ENSP00000370113.3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82148 AN: 151850 Hom.: 22544 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.531

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.541 AC: 82234 AN: 151968 Hom.: 22577 Cov.: 32 AF XY: 0.541 AC XY: 40171 AN XY: 74284

African (AFR) AF: 0.559 AC: 23151 AN: 41428

American (AMR) AF: 0.519 AC: 7928 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2299 AN: 5160

South Asian (SAS) AF: 0.503 AC: 2422 AN: 4816

European-Finnish (FIN) AF: 0.596 AC: 6288 AN: 10544

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37118 AN: 67960

Other (OTH) AF: 0.535 AC: 1128 AN: 2110

Alfa AF: 0.549 Hom.: 3863

Bravo AF: 0.535

Asia WGS AF: 0.484 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.48
PhyloP100		-0.91
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: rs17055106; hg19: chr8-26157848;