chr2-37628079-T-C

Variant names:

• chr2-37628079-T-C
• rs6729121
• ENST00000751737.1:n.619T>C

Variant summary

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

The ENST00000751737.1(CDC42EP3-AS1):​n.619T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,130 control chromosomes in the GnomAD database, including 38,833 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 0.71 (38833 hom., cov: 32)
• Consequence: CDC42EP3-AS1 ENST00000751737.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42EP3-AS1	ENST00000751737.1	n.619T>C		non_coding_transcript_exon_variant	Exon 2 of 2
CDC42EP3-AS1	ENST00000419425.1	n.314-14662T>C		intron_variant	Intron 2 of 4	3
CDC42EP3-AS1	ENST00000702971.2	n.104+10648T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107735 AN: 152012 Hom.: 38790 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.709 AC: 107833 AN: 152130 Hom.: 38833 Cov.: 32 AF XY: 0.711 AC XY: 52909 AN XY: 74368

African (AFR) AF: 0.827 AC: 34300 AN: 41498

American (AMR) AF: 0.681 AC: 10398 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4884 AN: 5184

South Asian (SAS) AF: 0.688 AC: 3318 AN: 4824

European-Finnish (FIN) AF: 0.691 AC: 7306 AN: 10576

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43229 AN: 67982

Other (OTH) AF: 0.677 AC: 1432 AN: 2114

Alfa AF: 0.654 Hom.: 53902

Bravo AF: 0.716

Asia WGS AF: 0.812 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.82
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6729121; hg19: chr2-37855222;