chr2-37504522-G-A

Variant names:

• chr2-37504522-G-A
• rs960902
• ENST00000668683.1:n.255-19447G>A

Variant summary

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

The ENST00000668683.1(CDC42EP3-AS1):​n.255-19447G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,814 control chromosomes in the GnomAD database, including 20,193 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 0.51 (20193 hom., cov: 31)
• Consequence: CDC42EP3-AS1 ENST00000668683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 7 publications found

Genes affected

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

ENSG00000298063 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668683.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42EP3-AS1	ENST00000668683.1		n.255-19447G>A		intron	N/A
	CDC42EP3-AS1	ENST00000686061.2		n.163+14941G>A		intron	N/A
	CDC42EP3-AS1	ENST00000689279.2		n.148+14941G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77953 AN: 151696 Hom.: 20172 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.514 AC: 78025 AN: 151814 Hom.: 20193 Cov.: 31 AF XY: 0.518 AC XY: 38413 AN XY: 74186

African (AFR) AF: 0.545 AC: 22556 AN: 41358

American (AMR) AF: 0.566 AC: 8632 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1771 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2102 AN: 5164

South Asian (SAS) AF: 0.441 AC: 2119 AN: 4806

European-Finnish (FIN) AF: 0.534 AC: 5619 AN: 10518

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33554 AN: 67938

Other (OTH) AF: 0.508 AC: 1071 AN: 2110

Alfa AF: 0.498 Hom.: 80183

Bravo AF: 0.518

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.25
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs960902; hg19: chr2-37731665;