rs3751928

Variant names:

• chr17-73285213-A-C
• rs3751928
• NM_012121.5:c.*217T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-73285213-A-C
• chr17-73285213-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_012121.5(CDC42EP4):​c.*217T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CDC42EP4 NM_012121.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 9 publications found

Genes affected

CDC42EP4 (HGNC:17147): (CDC42 effector protein 4) The product of this gene is a member of the CDC42-binding protein family. Members of this family interact with Rho family GTPases and regulate the organization of the actin cytoskeleton. This protein has been shown to bind both CDC42 and TC10 GTPases in a GTP-dependent manner. When overexpressed in fibroblasts, this protein was able to induce pseudopodia formation, which suggested a role in inducing actin filament assembly and cell shape control. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC42EP4	NM_012121.5	c.*217T>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000335793.4	NP_036253.2
CDC42EP4	XM_005257182.3	c.*217T>G		3_prime_UTR_variant	Exon 2 of 2		XP_005257239.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42EP4	ENST00000335793.4	c.*217T>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_012121.5	ENSP00000338258.3
CDC42EP4	ENST00000439510.2	c.*217T>G		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000404270.2
CDC42EP4	ENST00000581014.1	c.*245T>G		3_prime_UTR_variant	Exon 3 of 3	5		ENSP00000464104.1
CDC42EP4	ENST00000630622.1	c.*245T>G		downstream_gene_variant		5		ENSP00000485861.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 3

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 45778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.24
DANN	Benign	0.32
PhyloP100		-0.75

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

Other links and lift over

dbSNP: rs3751928; hg19: chr17-71281352;