chr20-48707172-C-T

Position:

• chr20-48707172-C-T

Variant summary

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

The ENST00000371941.4(PREX1):​c.783+1088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,170 control chromosomes in the GnomAD database, including 9,478 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 0.30 (9478 hom., cov: 32)
• Consequence: PREX1 ENST00000371941.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PREX1	NM_020820.4	c.783+1088G>A		intron_variant		ENST00000371941.4	NP_065871.3
PREX1	XM_047440331.1	c.258+1088G>A		intron_variant			XP_047296287.1
PREX1	XM_047440332.1	c.258+1088G>A		intron_variant			XP_047296288.1
PREX1	XM_047440333.1	c.258+1088G>A		intron_variant			XP_047296289.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PREX1	ENST00000371941.4	c.783+1088G>A		intron_variant		1	NM_020820.4	ENSP00000361009	P1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46240 AN: 152050 Hom.: 9458 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.304 AC: 46296 AN: 152170 Hom.: 9478 Cov.: 32 AF XY: 0.299 AC XY: 22287 AN XY: 74416

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0937

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.281

Alfa AF: 0.259 Hom.: 789

Bravo AF: 0.318

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.77

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: rs736659; hg19: chr20-47323710;