20-48681001-G-A

Variant names:

• chr20-48681001-G-A
• rs6095239
• NM_020820.4:c.1435+234C>T

Variant summary

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

The NM_020820.4(PREX1):​c.1435+234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,998 control chromosomes in the GnomAD database, including 12,003 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 0.39 (12003 hom., cov: 32)
• Consequence: PREX1 NM_020820.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 7 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020820.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PREX1	NM_020820.4	MANE Select	c.1435+234C>T		intron	N/A	NP_065871.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PREX1	ENST00000371941.4	TSL:1 MANE Select	c.1435+234C>T		intron	N/A	ENSP00000361009.3

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58758 AN: 151880 Hom.: 11984 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.387 AC: 58808 AN: 151998 Hom.: 12003 Cov.: 32 AF XY: 0.388 AC XY: 28834 AN XY: 74310

African (AFR) AF: 0.514 AC: 21302 AN: 41448

American (AMR) AF: 0.442 AC: 6755 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1828 AN: 5160

South Asian (SAS) AF: 0.532 AC: 2561 AN: 4812

European-Finnish (FIN) AF: 0.254 AC: 2684 AN: 10582

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21036 AN: 67950

Other (OTH) AF: 0.413 AC: 870 AN: 2104

Alfa AF: 0.340 Hom.: 39911

Bravo AF: 0.398

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.89
DANN	Benign	0.57
PhyloP100		-0.32
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: rs6095239; hg19: chr20-47297539;