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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985869	XR_001739409.2	n.234+5377G>T		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+5377G>T		intron_variant	Intron 4 of 5
CDC42EP3-AS1	ENST00000751610.1	n.515+5377G>T		intron_variant	Intron 4 of 4
CDC42EP3-AS1	ENST00000751628.1	n.46+5377G>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs604381; hg19: chr2-37977017;