ENST00000668683.1:n.255-23882G>A

Variant names:

• chr2-37500087-G-A
• rs7574012
• ENST00000668683.1:n.255-23882G>A

Variant summary

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

The ENST00000668683.1(CDC42EP3-AS1):​n.255-23882G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,964 control chromosomes in the GnomAD database, including 17,273 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 0.47 (17273 hom., cov: 32)
• Consequence: CDC42EP3-AS1 ENST00000668683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.571 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42EP3-AS1	ENST00000668683.1		n.255-23882G>A		intron	N/A
	CDC42EP3-AS1	ENST00000686061.2		n.163+10506G>A		intron	N/A
	CDC42EP3-AS1	ENST00000689279.2		n.148+10506G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71966 AN: 151846 Hom.: 17256 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.474 AC: 72023 AN: 151964 Hom.: 17273 Cov.: 32 AF XY: 0.472 AC XY: 35061 AN XY: 74268

African (AFR) AF: 0.534 AC: 22164 AN: 41470

American (AMR) AF: 0.410 AC: 6249 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3472

East Asian (EAS) AF: 0.589 AC: 3039 AN: 5160

South Asian (SAS) AF: 0.510 AC: 2460 AN: 4828

European-Finnish (FIN) AF: 0.448 AC: 4725 AN: 10558

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30241 AN: 67934

Other (OTH) AF: 0.471 AC: 991 AN: 2104

Alfa AF: 0.458 Hom.: 2754

Bravo AF: 0.474

Asia WGS AF: 0.525 AC: 1827 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	1.8
DANN	Benign	0.28
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7574012; hg19: chr2-37727230;