rs6733708

Positions:

• chr2-37733569-G-A

Variant summary

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

The XR_939971.3(LOC105374465):​n.170+3834C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 146,246 control chromosomes in the GnomAD database, including 13,849 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 0.41 (13849 hom., cov: 24)
• Consequence: LOC105374465 XR_939971.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

Genes affected

LOC105374465 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374465	XR_939971.3	n.170+3834C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDC42EP3	ENST00000453555.1	c.-740+4790C>T		intron_variant		3		ENSP00000398062

Frequencies

GnomAD3 genomes AF: 0.412 AC: 60257 AN: 146202 Hom.: 13835 Cov.: 24

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.412 AC: 60296 AN: 146246 Hom.: 13849 Cov.: 24 AF XY: 0.408 AC XY: 28952 AN XY: 70940

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.398

Alfa AF: 0.433 Hom.: 1724

Bravo AF: 0.418

Asia WGS AF: 0.219 AC: 717 AN: 3282

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6733708; hg19: chr2-37960712;