rs549433

Positions:

• chr12-62787036-T-C

Variant summary

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

The NM_020700.2(PPM1H):​c.869+1190A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 152,106 control chromosomes in the GnomAD database, including 10,816 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 0.36 (10816 hom., cov: 32)
• Consequence: PPM1H NM_020700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

Genes affected

PPM1H (HGNC:18583): (protein phosphatase, Mg2+/Mn2+ dependent 1H) Enables identical protein binding activity and phosphoprotein phosphatase activity. Predicted to be involved in protein dephosphorylation. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPM1H	NM_020700.2	c.869+1190A>G		intron_variant		ENST00000228705.7
PPM1H	XM_011538578.3	c.755+1190A>G		intron_variant
PPM1H	XM_017019676.3	c.869+1190A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPM1H	ENST00000228705.7	c.869+1190A>G		intron_variant		1	NM_020700.2	P1
PPM1H	ENST00000551519.1	n.259+1190A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54777 AN: 151986 Hom.: 10786 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.361 AC: 54855 AN: 152106 Hom.: 10816 Cov.: 32 AF XY: 0.360 AC XY: 26786 AN XY: 74354

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.342

Alfa AF: 0.303 Hom.: 15111

Bravo AF: 0.357

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs549433; hg19: chr12-63180816;