11-16880721-C-T

Variant summary

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

The NM_001329630.2(PLEKHA7):c.222-9539G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,130 control chromosomes in the GnomAD database, including 4,678 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 0.24 (4678 hom., cov: 33)
• Consequence: PLEKHA7 NM_001329630.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826

Genes affected

PLEKHA7 (HGNC:27049): (pleckstrin homology domain containing A7) Enables delta-catenin binding activity. Involved in epithelial cell-cell adhesion; pore complex assembly; and zonula adherens maintenance. Located in several cellular components, including centrosome; nucleoplasm; and zonula adherens. Part of pore complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLEKHA7	NM_001329630.2	c.222-9539G>A		intron_variant		ENST00000531066.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLEKHA7	ENST00000531066.6	c.222-9539G>A		intron_variant		5	NM_001329630.2	A1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36639 AN: 152012 Hom.: 4673 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.241 AC: 36675 AN: 152130 Hom.: 4678 Cov.: 33 AF XY: 0.238 AC XY: 17727 AN XY: 74362

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.235

Alfa AF: 0.271 Hom.: 10293

Bravo AF: 0.240

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.8
Dann	Benign	0.76

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: rs381815; hg19: chr11-16902268;