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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377326	XR_938964.2	n.*191C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPM1K-DT	ENST00000726976.1	n.282-7842C>T		intron_variant	Intron 2 of 2
PPM1K-DT	ENST00000726977.1	n.231-7842C>T		intron_variant	Intron 2 of 2
PPM1K-DT	ENST00000726978.1	n.344-7842C>T		intron_variant	Intron 3 of 3

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 v4.3

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;