rs13391045

Variant names:

• chr2-37711842-T-C
• rs13391045
• ENST00000453555.1:c.-333+7696A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-37711842-T-C
• chr2-37711842-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

CDC42EP3-AS1 (HGNC:56370): (CDC42EP3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42EP3	ENST00000453555.1	c.-333+7696A>G		intron_variant	Intron 2 of 3	3		ENSP00000398062.1
CDC42EP3-AS1	ENST00000751609.1	n.470-32610T>C		intron_variant	Intron 3 of 5
CDC42EP3-AS1	ENST00000751610.1	n.470-32610T>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.198 AC: 8225 AN: 41502

American (AMR) AF: 0.211 AC: 3230 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3472

East Asian (EAS) AF: 0.0354 AC: 183 AN: 5172

South Asian (SAS) AF: 0.0893 AC: 430 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3341 AN: 10534

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19968 AN: 67968

Other (OTH) AF: 0.250 AC: 528 AN: 2116

Alfa AF: 0.269 Hom.: 21908

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
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs13391045; hg19: chr2-37938985;