rs9995093

chr4-88299792-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134238.1(PPM1K-DT):n.133-12004T>A variant causes a intron, non coding transcript 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 NR_134238.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PPM1K-DT	NR_134238.1	n.133-12004T>A		intron_variant, non_coding_transcript_variant
PPM1K-DT	NR_134236.1	n.133-12004T>A		intron_variant, non_coding_transcript_variant
PPM1K-DT	NR_134237.1	n.132+14731T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPM1K-DT	ENST00000686365.2	n.179+14731T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.0945

Gnomad4 ASJ AF: 0.0978

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0722

Gnomad4 NFE AF: 0.0701

Gnomad4 OTH AF: 0.0948

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9995093; hg19: chr4-89220944;