ENST00000566543.1:c.-55+164T>C

Variant names:

• chr16-66878803-T-C
• rs149156
• ENST00000566543.1:c.-55+164T>C

Variant summary

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

The ENST00000566543.1(PDP2):​c.-55+164T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,978 control chromosomes in the GnomAD database, including 29,247 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 0.60 (29247 hom., cov: 31)
• Consequence: PDP2 ENST00000566543.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 11 publications found

Genes affected

PDP2 (HGNC:30263): (pyruvate dehydrogenase phosphatase catalytic subunit 2) This gene is a mitochondrial protein that functions as a phosphatase and is involved in the enzymatic resetting of the pyruvate dehydrogenase complex. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566543.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDP2	ENST00000566543.1	TSL:4	c.-55+164T>C		intron	N/A	ENSP00000457331.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91563 AN: 151858 Hom.: 29190 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.603 AC: 91683 AN: 151978 Hom.: 29247 Cov.: 31 AF XY: 0.603 AC XY: 44780 AN XY: 74264

African (AFR) AF: 0.819 AC: 33937 AN: 41458

American (AMR) AF: 0.590 AC: 8997 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3242 AN: 5154

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4812

European-Finnish (FIN) AF: 0.486 AC: 5138 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33473 AN: 67944

Other (OTH) AF: 0.593 AC: 1247 AN: 2104

Alfa AF: 0.534 Hom.: 93909

Bravo AF: 0.622

Asia WGS AF: 0.643 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.18
PhyloP100		-2.9
PromoterAI		0.00070	Neutral

Splicing

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

Other links and lift over

dbSNP: rs149156; hg19: chr16-66912706;