ENST00000500009.3:n.127-6526T>C

Variant names:

• chr4-88305270-T-C
• rs1440581
• ENST00000500009.3:n.127-6526T>C

Variant summary

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

The ENST00000500009.3(PPM1K-DT):​n.127-6526T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,042 control chromosomes in the GnomAD database, including 25,179 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 0.57 (25179 hom., cov: 32)
• Consequence: PPM1K-DT ENST00000500009.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 68 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPM1K-DT	NR_134236.1	n.133-6526T>C		intron_variant	Intron 1 of 4
PPM1K-DT	NR_134237.1	n.133-11416T>C		intron_variant	Intron 1 of 3
PPM1K-DT	NR_134238.1	n.133-6526T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPM1K-DT	ENST00000500009.3	n.127-6526T>C		intron_variant	Intron 1 of 4	1
PPM1K-DT	ENST00000652965.1	n.311-6526T>C		intron_variant	Intron 1 of 4
PPM1K-DT	ENST00000661337.1	n.81-6526T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86682 AN: 151924 Hom.: 25141 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.571 AC: 86776 AN: 152042 Hom.: 25179 Cov.: 32 AF XY: 0.567 AC XY: 42134 AN XY: 74308

African (AFR) AF: 0.696 AC: 28862 AN: 41486

American (AMR) AF: 0.524 AC: 8009 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2095 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2696 AN: 5154

South Asian (SAS) AF: 0.473 AC: 2276 AN: 4810

European-Finnish (FIN) AF: 0.472 AC: 4990 AN: 10562

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 36043 AN: 67964

Other (OTH) AF: 0.556 AC: 1173 AN: 2110

Alfa AF: 0.545 Hom.: 94263

Bravo AF: 0.579

Asia WGS AF: 0.517 AC: 1801 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	0.72
DANN	Benign	0.60
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1440581; hg19: chr4-89226422;