2-44127356-G-A

Variant names:

• chr2-44127356-G-A
• rs896986
• ENST00000727114.1:n.141-10423C>T

Variant summary

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

The ENST00000727114.1(PPM1B-DT):​n.141-10423C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,082 control chromosomes in the GnomAD database, including 20,195 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 0.51 (20195 hom., cov: 33)
• Consequence: PPM1B-DT ENST00000727114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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.141-10423C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77907 AN: 151964 Hom.: 20173 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.513 AC: 77979 AN: 152082 Hom.: 20195 Cov.: 33 AF XY: 0.511 AC XY: 37951 AN XY: 74338

African (AFR) AF: 0.593 AC: 24590 AN: 41456

American (AMR) AF: 0.395 AC: 6041 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2549 AN: 5184

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4820

European-Finnish (FIN) AF: 0.503 AC: 5313 AN: 10566

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33988 AN: 67994

Other (OTH) AF: 0.495 AC: 1043 AN: 2108

Alfa AF: 0.501 Hom.: 52644

Bravo AF: 0.508

Asia WGS AF: 0.514 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.017
DANN	Benign	0.48
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs896986; hg19: chr2-44354495;