rs13012266

Variant names:

• chr2-37730337-T-C
• rs13012266
• ENST00000453555.1:c.-740+8022A>G

Variant summary

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

The ENST00000453555.1(CDC42EP3):​c.-740+8022A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,134 control chromosomes in the GnomAD database, including 6,097 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 0.25 (6097 hom., cov: 32)
• Consequence: CDC42EP3 ENST00000453555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 1 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)

LOC105374465 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453555.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42EP3	ENST00000453555.1	TSL:3	c.-740+8022A>G		intron	N/A	ENSP00000398062.1
	CDC42EP3-AS1	ENST00000751609.1		n.470-14115T>C		intron	N/A
	CDC42EP3-AS1	ENST00000751610.1		n.470-14115T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38251 AN: 152016 Hom.: 6065 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.252 AC: 38341 AN: 152134 Hom.: 6097 Cov.: 32 AF XY: 0.249 AC XY: 18529 AN XY: 74416

African (AFR) AF: 0.442 AC: 18311 AN: 41462

American (AMR) AF: 0.217 AC: 3323 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.0287 AC: 149 AN: 5190

South Asian (SAS) AF: 0.376 AC: 1816 AN: 4826

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10600

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11906 AN: 67978

Other (OTH) AF: 0.233 AC: 493 AN: 2114

Alfa AF: 0.222 Hom.: 563

Bravo AF: 0.261

Asia WGS AF: 0.213 AC: 741 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.83
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs13012266; hg19: chr2-37957480;