5-131362781-C-A

Position:

• chr5-131362781-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375635.1(CDC42SE2):​c.54+3234C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,030 control chromosomes in the GnomAD database, including 4,314 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 0.23 (4314 hom., cov: 31)
• Consequence: CDC42SE2 NM_001375635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

CDC42SE2 (HGNC:18547): (CDC42 small effector 2) Enables signaling adaptor activity. Involved in regulation of signal transduction. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDC42SE2	NM_001375635.1	c.54+3234C>A		intron_variant		ENST00000505065.2	NP_001362564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDC42SE2	ENST00000505065.2	c.54+3234C>A		intron_variant		1	NM_001375635.1	ENSP00000427421	P1
CDC42SE2	ENST00000360515.7	c.54+3234C>A		intron_variant		1		ENSP00000353706	P1
CDC42SE2	ENST00000503291.5	c.-28+3223C>A		intron_variant		1		ENSP00000426779
CDC42SE2	ENST00000395246.5	c.54+3234C>A		intron_variant		5		ENSP00000378667	P1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34319 AN: 151912 Hom.: 4310 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.226 AC: 34353 AN: 152030 Hom.: 4314 Cov.: 31 AF XY: 0.236 AC XY: 17556 AN XY: 74310

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.213

Alfa AF: 0.146 Hom.: 348

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.89
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs798412; hg19: chr5-130698474;