rs13391045

chr2-37711842-T-Cchr2-37711842-T-G

Variant summary

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

The ENST00000453555.1(CDC42EP3):c.-333+7696A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,062 control chromosomes in the GnomAD database, including 4,911 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 (4911 hom., cov: 32)
• Consequence: CDC42EP3 ENST00000453555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626

Genes affected

CDC42EP3 (HGNC:16943): (CDC42 effector protein 3) This gene encodes a member of a small family of guanosine triphosphate (GTP) metabolizing proteins that contain a CRIB (Cdc42, Rac interactive binding) domain. Members of this family of proteins act as effectors of CDC42 function. The encoded protein is involved in actin cytoskeleton re-organization during cell shape changes, including pseudopodia formation. A pseudogene of this gene is found on chromosome 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC42EP3	ENST00000453555.1	c.-333+7696A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36899 AN: 151944 Hom.: 4911 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0353

Gnomad SAS AF: 0.0895

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.243 AC: 36911 AN: 152062 Hom.: 4911 Cov.: 32 AF XY: 0.239 AC XY: 17738 AN XY: 74320

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0354

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.250

Alfa AF: 0.275 Hom.: 8948

Bravo AF: 0.233

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	8.7
Dann	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13391045; hg19: chr2-37938985;