chr2-37752757-G-A

Variant names:

• chr2-37752757-G-A
• rs543852
• ENST00000751609.1:n.515+8260G>A

Variant summary

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

The ENST00000751609.1(CDC42EP3-AS1):​n.515+8260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,924 control chromosomes in the GnomAD database, including 21,693 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 0.53 (21693 hom., cov: 31)
• Consequence: CDC42EP3-AS1 ENST00000751609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 6 publications found

Genes affected

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

ENSG00000297981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751609.1. 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	ENST00000751609.1		n.515+8260G>A		intron	N/A
	CDC42EP3-AS1	ENST00000751610.1		n.515+8260G>A		intron	N/A
	CDC42EP3-AS1	ENST00000751628.1		n.46+8260G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80409 AN: 151806 Hom.: 21676 Cov.: 31

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.530 AC: 80467 AN: 151924 Hom.: 21693 Cov.: 31 AF XY: 0.531 AC XY: 39431 AN XY: 74256

African (AFR) AF: 0.427 AC: 17681 AN: 41392

American (AMR) AF: 0.549 AC: 8381 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2771 AN: 5158

South Asian (SAS) AF: 0.691 AC: 3332 AN: 4820

European-Finnish (FIN) AF: 0.576 AC: 6078 AN: 10554

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38359 AN: 67948

Other (OTH) AF: 0.552 AC: 1166 AN: 2112

Alfa AF: 0.551 Hom.: 2642

Bravo AF: 0.515

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs543852; hg19: chr2-37979900;