rs10113275

Positions:

• chr8-38903665-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021623.2(PLEKHA2):​c.-24+2220C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,130 control chromosomes in the GnomAD database, including 3,470 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 (3470 hom., cov: 32)
• Consequence: PLEKHA2 NM_021623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

PLEKHA2 (HGNC:14336): (pleckstrin homology domain containing A2) Enables fibronectin binding activity; laminin binding activity; and phosphatidylinositol-3,4-bisphosphate binding activity. Involved in positive regulation of cell-matrix adhesion. Located in cytoplasm and membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLEKHA2	NM_021623.2	c.-24+2220C>G		intron_variant		ENST00000617275.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLEKHA2	ENST00000617275.5	c.-24+2220C>G		intron_variant		2	NM_021623.2	P1

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32047 AN: 152012 Hom.: 3465 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.211 AC: 32069 AN: 152130 Hom.: 3470 Cov.: 32 AF XY: 0.209 AC XY: 15575 AN XY: 74384

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.0125

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.195

Alfa AF: 0.205 Hom.: 387

Bravo AF: 0.216

Asia WGS AF: 0.107 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs10113275; hg19: chr8-38761183;