rs7943587

Variant names:

• chr11-16793084-C-A
• rs7943587
• NM_001329630.2:c.2745+1404G>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.2745+1404G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,206 control chromosomes in the GnomAD database, including 2,738 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 0.18 (2738 hom., cov: 33)
• Consequence: PLEKHA7 NM_001329630.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.272 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.2745+1404G>T		intron	N/A	NP_001316559.1
	PLEKHA7	NM_001410960.1		c.2745+1404G>T		intron	N/A	NP_001397889.1
	PLEKHA7	NM_001329631.2		c.2745+1404G>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.2745+1404G>T		intron	N/A	ENSP00000435389.1
	PLEKHA7	ENST00000355661.7	TSL:1	c.2745+1404G>T		intron	N/A	ENSP00000347883.2
	PLEKHA7	ENST00000530489.5	TSL:1	c.1635+1404G>T		intron	N/A	ENSP00000433467.1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27536 AN: 152088 Hom.: 2738 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.181 AC: 27552 AN: 152206 Hom.: 2738 Cov.: 33 AF XY: 0.185 AC XY: 13791 AN XY: 74428

African (AFR) AF: 0.144 AC: 5986 AN: 41524

American (AMR) AF: 0.279 AC: 4269 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1443 AN: 5178

South Asian (SAS) AF: 0.180 AC: 868 AN: 4824

European-Finnish (FIN) AF: 0.184 AC: 1948 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12151 AN: 68006

Other (OTH) AF: 0.163 AC: 344 AN: 2116

Alfa AF: 0.181 Hom.: 379

Bravo AF: 0.185

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		0.27
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: rs7943587; hg19: chr11-16814631;