ENST00000751609.1:n.516-57510T>C

Variant names:

• chr2-37809274-T-C
• rs10495874
• ENST00000751609.1:n.516-57510T>C

Variant summary

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

The ENST00000751609.1(CDC42EP3-AS1):​n.516-57510T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,268 control chromosomes in the GnomAD database, including 1,368 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 0.13 (1368 hom., cov: 32)
• Consequence: CDC42EP3-AS1 ENST00000751609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08
• Publications: 3 publications found

Genes affected

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

PIRAT1 (HGNC:37459): (PU.1 (SPI1) induced regulator of S100A8 and S100A9 alarmin transcription 1)

ENSG00000298011 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42EP3-AS1	ENST00000751609.1		n.516-57510T>C		intron	N/A
	CDC42EP3-AS1	ENST00000751628.1		n.47-57510T>C		intron	N/A
	PIRAT1	ENST00000751985.1		n.304-22474A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19365 AN: 152150 Hom.: 1370 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00770

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.127 AC: 19375 AN: 152268 Hom.: 1368 Cov.: 32 AF XY: 0.127 AC XY: 9421 AN XY: 74460

African (AFR) AF: 0.108 AC: 4490 AN: 41538

American (AMR) AF: 0.0982 AC: 1502 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3472

East Asian (EAS) AF: 0.00772 AC: 40 AN: 5184

South Asian (SAS) AF: 0.191 AC: 923 AN: 4826

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10608

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10296 AN: 68018

Other (OTH) AF: 0.133 AC: 282 AN: 2116

Alfa AF: 0.148 Hom.: 868

Bravo AF: 0.122

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs10495874; hg19: chr2-38036417;