2-37733470-A-T

Position:

• chr2-37733470-A-T

Variant summary

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

The XR_939971.3(LOC105374465):​n.170+3933T>A 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 0.056 in 152,162 control chromosomes in the GnomAD database, including 331 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 0.056 (331 hom., cov: 31)
• Consequence: LOC105374465 XR_939971.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.085 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374465	XR_939971.3	n.170+3933T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC42EP3	ENST00000453555.1	c.-740+4889T>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0560 AC: 8517 AN: 152044 Hom.: 331 Cov.: 31

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0560 AC: 8516 AN: 152162 Hom.: 331 Cov.: 31 AF XY: 0.0543 AC XY: 4037 AN XY: 74402

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.0682

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0352 Hom.: 12

Bravo AF: 0.0522

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17511102; hg19: chr2-37960613;