11-16987058-T-C

Variant names:

• chr11-16987058-T-C
• rs11024102
• NM_001329630.2:c.221+26931A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001329630.2(PLEKHA7):​c.221+26931A>G variant causes a intron change. The variant allele was found at a frequency of 0.21 in 152,130 control chromosomes in the GnomAD database, including 4,242 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 0.21 (4242 hom., cov: 33)
• Consequence: PLEKHA7 NM_001329630.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.64
• Publications: 58 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLEKHA7	NM_001329630.2	c.221+26931A>G		intron_variant	Intron 3 of 26	ENST00000531066.6	NP_001316559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLEKHA7	ENST00000531066.6	c.221+26931A>G		intron_variant	Intron 3 of 26	5	NM_001329630.2	ENSP00000435389.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31924 AN: 152012 Hom.: 4246 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.210 AC: 31923 AN: 152130 Hom.: 4242 Cov.: 33 AF XY: 0.211 AC XY: 15677 AN XY: 74346

African (AFR) AF: 0.0531 AC: 2208 AN: 41546

American (AMR) AF: 0.236 AC: 3601 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3466

East Asian (EAS) AF: 0.387 AC: 1995 AN: 5152

South Asian (SAS) AF: 0.333 AC: 1605 AN: 4818

European-Finnish (FIN) AF: 0.256 AC: 2705 AN: 10568

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18502 AN: 67970

Other (OTH) AF: 0.192 AC: 407 AN: 2116

Alfa AF: 0.256 Hom.: 24180

Bravo AF: 0.205

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	22
DANN	Benign	0.86
PhyloP100		3.6
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11024102; hg19: chr11-17008605;