2-37749874-G-T

Variant names:

• chr2-37749874-G-T
• rs604381
• ENST00000751609.1:n.515+5377G>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+5377G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,022 control chromosomes in the GnomAD database, including 13,353 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 0.39 (13353 hom., cov: 32)
• Consequence: CDC42EP3-AS1 ENST00000751609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42EP3-AS1	ENST00000751609.1		n.515+5377G>T		intron	N/A
	CDC42EP3-AS1	ENST00000751610.1		n.515+5377G>T		intron	N/A
	CDC42EP3-AS1	ENST00000751628.1		n.46+5377G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59405 AN: 151904 Hom.: 13312 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.391 AC: 59501 AN: 152022 Hom.: 13353 Cov.: 32 AF XY: 0.388 AC XY: 28863 AN XY: 74334

African (AFR) AF: 0.612 AC: 25343 AN: 41422

American (AMR) AF: 0.352 AC: 5385 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1305 AN: 3468

East Asian (EAS) AF: 0.0614 AC: 318 AN: 5180

South Asian (SAS) AF: 0.432 AC: 2084 AN: 4820

European-Finnish (FIN) AF: 0.277 AC: 2933 AN: 10582

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20748 AN: 67948

Other (OTH) AF: 0.388 AC: 819 AN: 2112

Alfa AF: 0.282 Hom.: 475

Bravo AF: 0.400

Asia WGS AF: 0.268 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.65
PhyloP100		0.53

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs604381;

hg19: chr2-37977017;