rs1887104

chr14-60273608-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021003.5(PPM1A):c.-20-9076T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,936 control chromosomes in the GnomAD database, including 5,797 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 0.27 (5797 hom., cov: 31)
• Consequence: PPM1A NM_021003.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

PPM1A (HGNC:9275): (protein phosphatase, Mg2+/Mn2+ dependent 1A) The protein encoded by this gene is a member of the PP2C family of Ser/Thr protein phosphatases. PP2C family members are known to be negative regulators of cell stress response pathways. This phosphatase dephosphorylates, and negatively regulates the activities of, MAP kinases and MAP kinase kinases. It has been shown to inhibit the activation of p38 and JNK kinase cascades induced by environmental stresses. This phosphatase can also dephosphorylate cyclin-dependent kinases, and thus may be involved in cell cycle control. Overexpression of this phosphatase is reported to activate the expression of the tumor suppressor gene TP53/p53, which leads to G2/M cell cycle arrest and apoptosis. Three alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPM1A	NM_021003.5	c.-20-9076T>G		intron_variant		ENST00000395076.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPM1A	ENST00000395076.9	c.-20-9076T>G		intron_variant		1	NM_021003.5	P1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40610 AN: 151816 Hom.: 5800 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.267 AC: 40627 AN: 151936 Hom.: 5797 Cov.: 31 AF XY: 0.264 AC XY: 19621 AN XY: 74280

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.254

Alfa AF: 0.251 Hom.: 3141

Bravo AF: 0.268

Asia WGS AF: 0.229 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	8.1
Dann	Benign	0.69

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

Other links and lift over

dbSNP: rs1887104; hg19: chr14-60740326;