chr11-16840936-C-A

Variant names:

• chr11-16840936-C-A
• rs429368
• NM_001329630.2:c.872+611G>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.872+611G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0963 in 152,112 control chromosomes in the GnomAD database, including 819 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 0.096 (819 hom., cov: 32)
• Consequence: PLEKHA7 NM_001329630.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLEKHA7	NM_001329630.2	MANE Select	c.872+611G>T		intron	N/A	NP_001316559.1	E9PKC0
	PLEKHA7	NM_001410960.1		c.872+611G>T		intron	N/A	NP_001397889.1	A0A8V8TMS3
	PLEKHA7	NM_001329631.2		c.872+611G>T		intron	N/A	NP_001316560.1	Q6IQ23-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLEKHA7	ENST00000531066.6	TSL:5 MANE Select	c.872+611G>T		intron	N/A	ENSP00000435389.1	E9PKC0
	PLEKHA7	ENST00000355661.7	TSL:1	c.872+611G>T		intron	N/A	ENSP00000347883.2	Q6IQ23-1
	PLEKHA7	ENST00000698836.1		c.872+611G>T		intron	N/A	ENSP00000513972.1	A0A8V8TMS3

Frequencies

GnomAD3 genomes AF: 0.0963 AC: 14641 AN: 151994 Hom.: 820 Cov.: 32

Gnomad AFR AF: 0.0483

Gnomad AMI AF: 0.0727

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0462

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.0963 AC: 14644 AN: 152112 Hom.: 819 Cov.: 32 AF XY: 0.0945 AC XY: 7030 AN XY: 74358

African (AFR) AF: 0.0483 AC: 2004 AN: 41492

American (AMR) AF: 0.140 AC: 2140 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3470

East Asian (EAS) AF: 0.159 AC: 819 AN: 5164

South Asian (SAS) AF: 0.117 AC: 562 AN: 4818

European-Finnish (FIN) AF: 0.0462 AC: 489 AN: 10586

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7789 AN: 67994

Other (OTH) AF: 0.115 AC: 242 AN: 2112

Alfa AF: 0.0471 Hom.: 38

Bravo AF: 0.105

Asia WGS AF: 0.130 AC: 452 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	3.8
DANN	Benign	0.57
PhyloP100		-0.050
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: rs429368; hg19: chr11-16862483;