chr4-88298493-G-A

Variant names:

• chr4-88298493-G-A
• rs10024717
• ENST00000500009.3:n.127-13303G>A

Variant summary

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

The ENST00000500009.3(PPM1K-DT):​n.127-13303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,066 control chromosomes in the GnomAD database, including 6,809 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 0.28 (6809 hom., cov: 33)
• Consequence: PPM1K-DT ENST00000500009.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 11 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500009.3. 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
	PPM1K-DT	NR_134236.1		n.133-13303G>A		intron	N/A
	PPM1K-DT	NR_134237.1		n.132+13432G>A		intron	N/A
	PPM1K-DT	NR_134238.1		n.133-13303G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1K-DT	ENST00000500009.3	TSL:1	n.127-13303G>A		intron	N/A
	PPM1K-DT	ENST00000652965.1		n.311-13303G>A		intron	N/A
	PPM1K-DT	ENST00000661337.1		n.81-13303G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43112 AN: 151948 Hom.: 6808 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0159

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.284 AC: 43123 AN: 152066 Hom.: 6809 Cov.: 33 AF XY: 0.277 AC XY: 20576 AN XY: 74328

African (AFR) AF: 0.184 AC: 7627 AN: 41454

American (AMR) AF: 0.253 AC: 3870 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1518 AN: 3468

East Asian (EAS) AF: 0.0160 AC: 83 AN: 5192

South Asian (SAS) AF: 0.167 AC: 808 AN: 4826

European-Finnish (FIN) AF: 0.308 AC: 3247 AN: 10550

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24932 AN: 67976

Other (OTH) AF: 0.294 AC: 620 AN: 2112

Alfa AF: 0.338 Hom.: 5792

Bravo AF: 0.273

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
DANN	Benign	0.47
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs10024717; hg19: chr4-89219645;