11-16958606-G-A

Variant names:

• chr11-16958606-G-A
• rs7121911
• NM_001329630.2:c.221+55383C>T

Variant summary

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

The NM_001329630.2(PLEKHA7):​c.221+55383C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,904 control chromosomes in the GnomAD database, including 19,484 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 0.50 (19484 hom., cov: 32)
• Consequence: PLEKHA7 NM_001329630.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329630.2. 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
	PLEKHA7	NM_001329630.2	MANE Select	c.221+55383C>T		intron	N/A	NP_001316559.1
	PLEKHA7	NM_001410960.1		c.221+55383C>T		intron	N/A	NP_001397889.1
	PLEKHA7	NM_001329631.2		c.221+55383C>T		intron	N/A	NP_001316560.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLEKHA7	ENST00000531066.6	TSL:5 MANE Select	c.221+55383C>T		intron	N/A	ENSP00000435389.1
	PLEKHA7	ENST00000355661.7	TSL:1	c.221+55383C>T		intron	N/A	ENSP00000347883.2
	PLEKHA7	ENST00000698836.1		c.221+55383C>T		intron	N/A	ENSP00000513972.1

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75725 AN: 151784 Hom.: 19463 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.499 AC: 75781 AN: 151904 Hom.: 19484 Cov.: 32 AF XY: 0.510 AC XY: 37892 AN XY: 74242

African (AFR) AF: 0.411 AC: 17008 AN: 41412

American (AMR) AF: 0.570 AC: 8694 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3826 AN: 5160

South Asian (SAS) AF: 0.741 AC: 3571 AN: 4822

European-Finnish (FIN) AF: 0.555 AC: 5837 AN: 10524

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33406 AN: 67940

Other (OTH) AF: 0.501 AC: 1057 AN: 2108

Alfa AF: 0.494 Hom.: 3234

Bravo AF: 0.492

Asia WGS AF: 0.702 AC: 2438 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.50
PhyloP100		0.14
Mutation Taster		=100/0	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: rs7121911; hg19: chr11-16980153; COSMIC: COSV63050475;