chr8-67973399-G-T

Variant names:

• chr8-67973399-G-T
• rs10504412
• NM_024870.4:c.141+20864G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024870.4(PREX2):​c.141+20864G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,982 control chromosomes in the GnomAD database, including 5,061 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 0.24 (5061 hom., cov: 32)
• Consequence: PREX2 NM_024870.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 2 publications found

Genes affected

PREX2 (HGNC:22950): (phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 2) The protein encoded by this gene belongs to the phosphatidylinositol 3,4,5-trisphosphate (PIP3)-dependent Rac exchanger (PREX) family, which are Dbl-type guanine-nucleotide exchange factors for Rac family small G proteins. Structural domains of this protein include the catalytic diffuse B-cell lymphoma homology and pleckstrin homology (DHPH) domain, two disheveled, EGL-10, and pleckstrin homology (DEP) domains, two PDZ domains, and a C-terminal inositol polyphosphate-4 phosphatase (IP4P) domain that is found in one of the isoforms. This protein facilitates the exchange of GDP for GTP on Rac1, allowing the GTP-bound Rac1 to activate downstream effectors. Studies also show that the pleckstrin homology domain of this protein interacts with the phosphatase and tensin homolog (PTEN) gene product to inhibit PTEN phosphatase activity, thus activating the phosphoinositide-3 kinase (PI3K) signaling pathway. Conversely, the PTEN gene product has also been shown to inhibit the GEF activity of this protein. This gene plays a role in insulin-signaling pathways, and either mutations or overexpression of this gene have been observed in some cancers. [provided by RefSeq, Apr 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PREX2	NM_024870.4	c.141+20864G>T		intron_variant	Intron 1 of 39	ENST00000288368.5	NP_079146.2
PREX2	NM_025170.6	c.141+20864G>T		intron_variant	Intron 1 of 23		NP_079446.3
PREX2	XM_047422268.1	c.141+20864G>T		intron_variant	Intron 1 of 27		XP_047278224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PREX2	ENST00000288368.5	c.141+20864G>T		intron_variant	Intron 1 of 39	1	NM_024870.4	ENSP00000288368.4
PREX2	ENST00000529398.5	n.168+20864G>T		intron_variant	Intron 1 of 23	1
PREX2	ENST00000517617.1	n.47+20864G>T		intron_variant	Intron 1 of 23	2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36458 AN: 151862 Hom.: 5060 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.240 AC: 36491 AN: 151982 Hom.: 5061 Cov.: 32 AF XY: 0.245 AC XY: 18203 AN XY: 74266

African (AFR) AF: 0.117 AC: 4834 AN: 41486

American (AMR) AF: 0.337 AC: 5144 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2784 AN: 5144

South Asian (SAS) AF: 0.377 AC: 1814 AN: 4810

European-Finnish (FIN) AF: 0.234 AC: 2468 AN: 10552

Middle Eastern (MID) AF: 0.255 AC: 74 AN: 290

European-Non Finnish (NFE) AF: 0.262 AC: 17819 AN: 67952

Other (OTH) AF: 0.273 AC: 577 AN: 2112

Alfa AF: 0.259 Hom.: 24355

Bravo AF: 0.245

Asia WGS AF: 0.432 AC: 1501 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.0080
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: rs10504412; hg19: chr8-68885634;