rs2421022

Positions:

• chr10-122404618-A-G
• chr10-122404618-A-T

Variant summary

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

The NM_001001974.4(PLEKHA1):​c.245-1958A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,110 control chromosomes in the GnomAD database, including 8,111 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 0.31 (8111 hom., cov: 32)
• Consequence: PLEKHA1 NM_001001974.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

Genes affected

PLEKHA1 (HGNC:14335): (pleckstrin homology domain containing A1) This gene encodes a pleckstrin homology domain-containing adapter protein. The encoded protein is localized to the plasma membrane where it specifically binds phosphatidylinositol 3,4-bisphosphate. This protein may be involved in the formation of signaling complexes in the plasma membrane. Polymorphisms in this gene are associated with age-related macular degeneration. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 5.[provided by RefSeq, Sep 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLEKHA1	NM_001001974.4	c.245-1958A>G		intron_variant		ENST00000368990.8	NP_001001974.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLEKHA1	ENST00000368990.8	c.245-1958A>G		intron_variant		1	NM_001001974.4	ENSP00000357986	P3

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47733 AN: 151992 Hom.: 8114 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.314 AC: 47744 AN: 152110 Hom.: 8111 Cov.: 32 AF XY: 0.307 AC XY: 22799 AN XY: 74350

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.345

Alfa AF: 0.211 Hom.: 479

Bravo AF: 0.308

Asia WGS AF: 0.235 AC: 819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.61

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: rs2421022; hg19: chr10-124164134;