ENST00000668683.1:n.255-132A>G

Variant names:

• chr2-37523837-A-G
• rs4352210
• ENST00000668683.1:n.255-132A>G

Variant summary

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

The ENST00000668683.1(CDC42EP3-AS1):​n.255-132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,882 control chromosomes in the GnomAD database, including 27,232 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 0.60 (27232 hom., cov: 31)
• Consequence: CDC42EP3-AS1 ENST00000668683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 16 publications found

Genes affected

CDC42EP3-AS1 (HGNC:56370): (CDC42EP3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668683.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42EP3-AS1	ENST00000668683.1		n.255-132A>G		intron	N/A
	CDC42EP3-AS1	ENST00000686061.2		n.164-13158A>G		intron	N/A
	CDC42EP3-AS1	ENST00000689279.2		n.149-13158A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90387 AN: 151762 Hom.: 27214 Cov.: 31

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.595 AC: 90441 AN: 151882 Hom.: 27232 Cov.: 31 AF XY: 0.598 AC XY: 44369 AN XY: 74214

African (AFR) AF: 0.548 AC: 22675 AN: 41408

American (AMR) AF: 0.639 AC: 9749 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1897 AN: 3466

East Asian (EAS) AF: 0.358 AC: 1842 AN: 5150

South Asian (SAS) AF: 0.477 AC: 2290 AN: 4800

European-Finnish (FIN) AF: 0.728 AC: 7697 AN: 10572

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.624 AC: 42369 AN: 67918

Other (OTH) AF: 0.586 AC: 1236 AN: 2108

Alfa AF: 0.605 Hom.: 90695

Bravo AF: 0.589

Asia WGS AF: 0.471 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.64
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs4352210; hg19: chr2-37750980;