rs435206

Variant names:

• chr11-16881631-C-A
• rs435206
• NM_001329630.2:c.222-10449G>T

Your query was ambiguous. Multiple possible variants found:

• chr11-16881631-C-A
• chr11-16881631-C-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.222-10449G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,148 control chromosomes in the GnomAD database, including 1,103 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 0.11 (1102 hom., cov: 32)
  • Exomes 𝑓: 0.093 (1 hom.)
• Consequence: PLEKHA7 NM_001329630.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLEKHA7	NM_001329630.2	c.222-10449G>T		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.222-10449G>T		intron_variant	Intron 3 of 26	5	NM_001329630.2	ENSP00000435389.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16581 AN: 151976 Hom.: 1103 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.137

GnomAD4 exome AF: 0.0926 AC: 5 AN: 54 Hom.: 1 Cov.: 0 AF XY: 0.0652 AC XY: 3 AN XY: 46

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 5 AN: 40

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.109 AC: 16582 AN: 152094 Hom.: 1102 Cov.: 32 AF XY: 0.109 AC XY: 8083 AN XY: 74326

African (AFR) AF: 0.0348 AC: 1446 AN: 41504

American (AMR) AF: 0.162 AC: 2476 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3470

East Asian (EAS) AF: 0.165 AC: 849 AN: 5154

South Asian (SAS) AF: 0.105 AC: 506 AN: 4808

European-Finnish (FIN) AF: 0.0926 AC: 980 AN: 10586

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9257 AN: 67988

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.0516 Hom.: 51

Bravo AF: 0.115

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.90
DANN	Benign	0.61
PhyloP100		-0.23
PromoterAI		0.0082	Neutral
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: rs435206; hg19: chr11-16903178;