2-37680992-A-G

Variant names:

• chr2-37680992-A-G
• rs2888542
• ENST00000453555.1:c.-236+7087T>C

Variant summary

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

The ENST00000453555.1(CDC42EP3):​c.-236+7087T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,108 control chromosomes in the GnomAD database, including 42,218 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 0.74 (42218 hom., cov: 32)
• Consequence: CDC42EP3 ENST00000453555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• 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)

LOC107985870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985870	XR_001739410.2	n.569+2140T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42EP3	ENST00000453555.1	c.-236+7087T>C		intron_variant	Intron 3 of 3	3		ENSP00000398062.1
CDC42EP3-AS1	ENST00000751609.1	n.470-63460A>G		intron_variant	Intron 3 of 5
CDC42EP3-AS1	ENST00000751610.1	n.470-63460A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112751 AN: 151990 Hom.: 42169 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.742 AC: 112857 AN: 152108 Hom.: 42218 Cov.: 32 AF XY: 0.747 AC XY: 55521 AN XY: 74350

African (AFR) AF: 0.797 AC: 33066 AN: 41488

American (AMR) AF: 0.779 AC: 11905 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2383 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4654 AN: 5186

South Asian (SAS) AF: 0.845 AC: 4072 AN: 4820

European-Finnish (FIN) AF: 0.685 AC: 7236 AN: 10562

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47131 AN: 67982

Other (OTH) AF: 0.740 AC: 1565 AN: 2114

Alfa AF: 0.710 Hom.: 71855

Bravo AF: 0.747

Asia WGS AF: 0.880 AC: 3056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.50
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2888542; hg19: chr2-37908135;