Variant rs2294910 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000371941.4(PREX1):c.1881+76T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,595,758 control chromosomes in the GnomAD database, including 31,108 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 0.18 ( 2457 hom., cov: 31)

Exomes 𝑓: 0.20 ( 28651 hom. )

Consequence

PREX1
ENST00000371941.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0470

Variant links:

Genes affected

PREX1 (HGNC:32594): (phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1) The protein encoded by this gene acts as a guanine nucleotide exchange factor for the RHO family of small GTP-binding proteins (RACs). It has been shown to bind to and activate RAC1 by exchanging bound GDP for free GTP. The encoded protein, which is found mainly in the cytoplasm, is activated by phosphatidylinositol-3,4,5-trisphosphate and the beta-gamma subunits of heterotrimeric G proteins. [provided by RefSeq, Jul 2008]

PREX1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PREX1	NM_020820.4 linkuse as main transcript	c.1881+76T>C		intron_variant		ENST00000371941.4	NP_065871.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PREX1	ENST00000371941.4 linkuse as main transcript	c.1881+76T>C		intron_variant		1	NM_020820.4	ENSP00000361009	P1	Q8TCU6-1

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26642

AN:

152010

Hom.:

2453

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.166

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.212

GnomAD4 exome

AF:

0.196

AC:

283022

AN:

1443630

Hom.:

28651

AF XY:

0.199

AC XY:

142639

AN XY:

717610

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.249

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.136

Gnomad4 SAS exome

AF:

0.265

Gnomad4 FIN exome

AF:

0.157

Gnomad4 NFE exome

AF:

0.194

Gnomad4 OTH exome

AF:

0.199

GnomAD4 genome

AF:

0.175

AC:

26666

AN:

152128

Hom.:

2457

Cov.:

AF XY:

0.175

AC XY:

13034

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.111

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.146

Gnomad4 SAS

AF:

0.276

Gnomad4 FIN

AF:

0.166

Gnomad4 NFE

AF:

0.193

Gnomad4 OTH

AF:

0.214

Alfa

AF:

0.197

Hom.:

6156

Bravo

AF:

0.173

Asia WGS

AF:

0.220

AC:

764

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.1

DANN

Benign

0.48

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over