ENST00000751609.1:n.515+31975A>G

Variant names:

• chr2-37776472-A-G
• rs10495872
• ENST00000751609.1:n.515+31975A>G

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+31975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,134 control chromosomes in the GnomAD database, including 1,837 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 0.14 (1837 hom., cov: 32)
• Consequence: CDC42EP3-AS1 ENST00000751609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 9 publications found

Genes affected

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

LOC107985869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985869	XR_001739409.2	n.235-8718A>G		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+31975A>G		intron_variant	Intron 4 of 5
CDC42EP3-AS1	ENST00000751610.1	n.516-8718A>G		intron_variant	Intron 4 of 4
CDC42EP3-AS1	ENST00000751628.1	n.46+31975A>G		intron_variant	Intron 1 of 3
CDC42EP3-AS1	ENST00000751712.1	n.102-8718A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21307 AN: 152016 Hom.: 1830 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.140 AC: 21349 AN: 152134 Hom.: 1837 Cov.: 32 AF XY: 0.146 AC XY: 10884 AN XY: 74374

African (AFR) AF: 0.102 AC: 4221 AN: 41512

American (AMR) AF: 0.246 AC: 3751 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3464

East Asian (EAS) AF: 0.341 AC: 1758 AN: 5152

South Asian (SAS) AF: 0.0991 AC: 478 AN: 4824

European-Finnish (FIN) AF: 0.186 AC: 1968 AN: 10580

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8134 AN: 68014

Other (OTH) AF: 0.153 AC: 322 AN: 2106

Alfa AF: 0.149 Hom.: 378

Bravo AF: 0.148

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.34
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10495872; hg19: chr2-38003615;