chr6-32877952-T-C

Variant names:

• chr6-32877952-T-C
• rs4959119

Variant summary

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

The variant allele was found at a frequency of 0.353 in 151,998 control chromosomes in the GnomAD database, including 9,648 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 0.35 (9648 hom., cov: 31)
• Consequence: PPP1R2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 8 publications found

Genes affected

PPP1R2P1 (HGNC:9289): (protein phosphatase 1 regulatory inhibitor subunit 2 pseudogene 1) Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in regulation of phosphoprotein phosphatase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53674 AN: 151880 Hom.: 9638 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.353 AC: 53715 AN: 151998 Hom.: 9648 Cov.: 31 AF XY: 0.347 AC XY: 25802 AN XY: 74310

African (AFR) AF: 0.364 AC: 15093 AN: 41444

American (AMR) AF: 0.381 AC: 5817 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5176

South Asian (SAS) AF: 0.268 AC: 1294 AN: 4828

European-Finnish (FIN) AF: 0.303 AC: 3197 AN: 10544

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24320 AN: 67948

Other (OTH) AF: 0.369 AC: 777 AN: 2104

Alfa AF: 0.362 Hom.: 1653

Bravo AF: 0.361

Asia WGS AF: 0.319 AC: 1110 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.2
DANN	Benign	0.73
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4959119; hg19: chr6-32845729; COSMIC: COSV105346472;