rs798416

chr5-131357407-T-Cchr5-131357407-T-G

Variant summary

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

The NM_001375635.1(CDC42SE2):c.-285-1802T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,112 control chromosomes in the GnomAD database, including 4,458 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 (4458 hom., cov: 32)
• Consequence: CDC42SE2 NM_001375635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

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=-0.88).
• 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	UniProt
CDC42SE2	NM_001375635.1	c.-285-1802T>C		intron_variant		ENST00000505065.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDC42SE2	ENST00000505065.2	c.-285-1802T>C		intron_variant		1	NM_001375635.1	P1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35230 AN: 151994 Hom.: 4453 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.232 AC: 35266 AN: 152112 Hom.: 4458 Cov.: 32 AF XY: 0.242 AC XY: 17990 AN XY: 74354

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.216

Alfa AF: 0.224 Hom.: 636

Bravo AF: 0.225

Asia WGS AF: 0.370 AC: 1287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.89
Dann	Benign	0.41

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: rs798416; hg19: chr5-130693100;