rs4693212

Variant names:

• chr4-88362344-C-T
• rs4693212
• ENST00000726976.1:n.282-7842C>T

Variant summary

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

The ENST00000726976.1(PPM1K-DT):​n.282-7842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,880 control chromosomes in the GnomAD database, including 5,540 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 0.25 (5540 hom., cov: 32)
• Consequence: PPM1K-DT ENST00000726976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 4 publications found

Genes affected

PPM1K-DT (HGNC:54093): (PPM1K divergent transcript)

LOC105377326 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726976.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1K-DT	ENST00000726976.1		n.282-7842C>T		intron	N/A
	PPM1K-DT	ENST00000726977.1		n.231-7842C>T		intron	N/A
	PPM1K-DT	ENST00000726978.1		n.344-7842C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38169 AN: 151762 Hom.: 5532 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.252 AC: 38203 AN: 151880 Hom.: 5540 Cov.: 32 AF XY: 0.258 AC XY: 19142 AN XY: 74218

African (AFR) AF: 0.142 AC: 5893 AN: 41420

American (AMR) AF: 0.298 AC: 4548 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3166 AN: 5160

South Asian (SAS) AF: 0.346 AC: 1667 AN: 4824

European-Finnish (FIN) AF: 0.289 AC: 3036 AN: 10516

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18267 AN: 67926

Other (OTH) AF: 0.249 AC: 524 AN: 2108

Alfa AF: 0.270 Hom.: 17842

Bravo AF: 0.249

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4693212; hg19: chr4-89283496;