2-44149387-A-G

Variant names:

• chr2-44149387-A-G
• rs2333821
• ENST00000727114.1:n.140+17911T>C

Variant summary

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

The ENST00000727114.1(PPM1B-DT):​n.140+17911T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,108 control chromosomes in the GnomAD database, including 44,015 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 0.76 (44015 hom., cov: 32)
• Consequence: PPM1B-DT ENST00000727114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 3 publications found

Genes affected

PPM1B-DT (HGNC:55161): (PPM1B divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727114.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1B-DT	ENST00000727114.1		n.140+17911T>C		intron	N/A
	PPM1B-DT	ENST00000727115.1		n.141-13979T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115237 AN: 151990 Hom.: 43983 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.758 AC: 115321 AN: 152108 Hom.: 44015 Cov.: 32 AF XY: 0.759 AC XY: 56412 AN XY: 74362

African (AFR) AF: 0.673 AC: 27909 AN: 41476

American (AMR) AF: 0.795 AC: 12160 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2824 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4461 AN: 5168

South Asian (SAS) AF: 0.878 AC: 4235 AN: 4826

European-Finnish (FIN) AF: 0.742 AC: 7851 AN: 10580

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53290 AN: 67976

Other (OTH) AF: 0.795 AC: 1680 AN: 2114

Alfa AF: 0.782 Hom.: 194632

Bravo AF: 0.755

Asia WGS AF: 0.849 AC: 2952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2333821; hg19: chr2-44376526;