rs12996442

Variant names:

• chr2-37775714-T-G
• rs12996442
• ENST00000751609.1:n.515+31217T>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+31217T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,230 control chromosomes in the GnomAD database, including 4,356 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 0.22 (4356 hom., cov: 32)
• Consequence: CDC42EP3-AS1 ENST00000751609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.32
• 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=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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+31217T>G		intron	N/A
	CDC42EP3-AS1	ENST00000751610.1		n.516-9476T>G		intron	N/A
	CDC42EP3-AS1	ENST00000751628.1		n.46+31217T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34178 AN: 152112 Hom.: 4352 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.225 AC: 34199 AN: 152230 Hom.: 4356 Cov.: 32 AF XY: 0.230 AC XY: 17112 AN XY: 74422

African (AFR) AF: 0.112 AC: 4647 AN: 41552

American (AMR) AF: 0.241 AC: 3686 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1265 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1320 AN: 5182

South Asian (SAS) AF: 0.132 AC: 638 AN: 4824

European-Finnish (FIN) AF: 0.348 AC: 3680 AN: 10586

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18048 AN: 68002

Other (OTH) AF: 0.238 AC: 503 AN: 2112

Alfa AF: 0.238 Hom.: 1679

Bravo AF: 0.212

Asia WGS AF: 0.187 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		3.3

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: rs12996442;

hg19: chr2-38002857;