ENST00000500009.3:n.127-12004T>A

Variant names:

• chr4-88299792-T-A
• rs9995093
• ENST00000500009.3:n.127-12004T>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.127-12004T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 152,256 control chromosomes in the GnomAD database, including 671 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 0.079 (671 hom., cov: 32)
• Consequence: PPM1K-DT ENST00000500009.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPM1K-DT	NR_134236.1	n.133-12004T>A		intron_variant	Intron 1 of 4
PPM1K-DT	NR_134237.1	n.132+14731T>A		intron_variant	Intron 1 of 3
PPM1K-DT	NR_134238.1	n.133-12004T>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPM1K-DT	ENST00000500009.3	n.127-12004T>A		intron_variant	Intron 1 of 4	1
PPM1K-DT	ENST00000652965.1	n.311-12004T>A		intron_variant	Intron 1 of 4
PPM1K-DT	ENST00000661337.1	n.81-12004T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0792 AC: 12054 AN: 152138 Hom.: 668 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0946

Gnomad ASJ AF: 0.0978

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0701

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0792 AC: 12058 AN: 152256 Hom.: 671 Cov.: 32 AF XY: 0.0808 AC XY: 6013 AN XY: 74434

African (AFR) AF: 0.0532 AC: 2209 AN: 41550

American (AMR) AF: 0.0945 AC: 1446 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0978 AC: 339 AN: 3466

East Asian (EAS) AF: 0.328 AC: 1697 AN: 5180

South Asian (SAS) AF: 0.105 AC: 507 AN: 4826

European-Finnish (FIN) AF: 0.0722 AC: 766 AN: 10606

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0701 AC: 4766 AN: 68014

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0702 Hom.: 56

Bravo AF: 0.0829

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.66
DANN	Benign	0.86
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs9995093; hg19: chr4-89220944;