chr2-158646504-G-A

Position:

• chr2-158646504-G-A

Variant summary

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

The NM_003628.6(PKP4):​c.1909+3805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,984 control chromosomes in the GnomAD database, including 16,377 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 0.45 (16377 hom., cov: 32)
• Consequence: PKP4 NM_003628.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

Genes affected

PKP4 (HGNC:9026): (plakophilin 4) Armadillo-like proteins are characterized by a series of armadillo repeats, first defined in the Drosophila 'armadillo' gene product, that are typically 42 to 45 amino acids in length. These proteins can be divided into subfamilies based on their number of repeats, their overall sequence similarity, and the dispersion of the repeats throughout their sequences. Members of the p120(ctn)/plakophilin subfamily of Armadillo-like proteins, including CTNND1, CTNND2, PKP1, PKP2, PKP4, and ARVCF. PKP4 may be a component of desmosomal plaque and other adhesion plaques and is thought to be involved in regulating junctional plaque organization and cadherin function. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKP4	NM_003628.6	c.1909+3805G>A		intron_variant		ENST00000389759.8	NP_003619.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKP4	ENST00000389759.8	c.1909+3805G>A		intron_variant		1	NM_003628.6	ENSP00000374409	P3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67751 AN: 151868 Hom.: 16359 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.446 AC: 67793 AN: 151984 Hom.: 16377 Cov.: 32 AF XY: 0.450 AC XY: 33386 AN XY: 74260

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.435

Alfa AF: 0.499 Hom.: 8766

Bravo AF: 0.445

Asia WGS AF: 0.584 AC: 2029 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.030
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs929390; hg19: chr2-159503016;