3-160882775-A-G

Variant names:

• chr3-160882775-A-G
• rs935497
• NM_139245.4:c.400-78961A>G

Variant summary

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

The NM_139245.4(PPM1L):​c.400-78961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,222 control chromosomes in the GnomAD database, including 5,658 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 (5658 hom., cov: 32)
• Consequence: PPM1L NM_139245.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 6 publications found

Genes affected

PPM1L (HGNC:16381): (protein phosphatase, Mg2+/Mn2+ dependent 1L) The protein encoded by this gene is a magnesium or manganese-requiring phosphatase that is involved in several signaling pathways. The encoded protein downregulates apoptosis signal-regulating kinase 1, a protein that initiates a signaling cascade that leads to apoptosis when cells are subjected to cytotoxic stresses. This protein also is an endoplasmic reticulum transmembrane protein that helps regulate ceramide transport from the endoplasmic reticulum to the Golgi apparatus. Finally, this gene may be involved in adiposity since it is upregulated in adipose tissues. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139245.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1L	NM_139245.4	MANE Select	c.400-78961A>G		intron	N/A	NP_640338.2
	PPM1L	NM_001317911.2		c.18+40483A>G		intron	N/A	NP_001304840.1
	PPM1L	NM_001317912.2		c.-239+40483A>G		intron	N/A	NP_001304841.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1L	ENST00000498165.6	TSL:1 MANE Select	c.400-78961A>G		intron	N/A	ENSP00000417659.1
	PPM1L	ENST00000295839.9	TSL:1	c.18+40483A>G		intron	N/A	ENSP00000295839.9
	PPM1L	ENST00000497343.5	TSL:2	c.400-78961A>G		intron	N/A	ENSP00000420354.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40385 AN: 152104 Hom.: 5660 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.265 AC: 40391 AN: 152222 Hom.: 5658 Cov.: 32 AF XY: 0.269 AC XY: 20018 AN XY: 74414

African (AFR) AF: 0.213 AC: 8859 AN: 41550

American (AMR) AF: 0.336 AC: 5141 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 858 AN: 3466

East Asian (EAS) AF: 0.510 AC: 2645 AN: 5182

South Asian (SAS) AF: 0.319 AC: 1537 AN: 4824

European-Finnish (FIN) AF: 0.249 AC: 2641 AN: 10588

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17833 AN: 68006

Other (OTH) AF: 0.263 AC: 557 AN: 2114

Alfa AF: 0.192 Hom.: 601

Bravo AF: 0.267

Asia WGS AF: 0.347 AC: 1206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.60
PhyloP100		-1.6
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: rs935497; hg19: chr3-160600563;