rs543852

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-37752757-G-A
• chr2-37752757-G-C
• chr2-37752757-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985869	XR_001739409.2	n.234+8260G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42EP3-AS1	ENST00000751609.1	n.515+8260G>A		intron_variant	Intron 4 of 5
CDC42EP3-AS1	ENST00000751610.1	n.515+8260G>A		intron_variant	Intron 4 of 4
CDC42EP3-AS1	ENST00000751628.1	n.46+8260G>A		intron_variant	Intron 1 of 3

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 v4.3

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;