5-131372351-C-G

Variant names:

• chr5-131372351-C-G
• rs40396
• NM_001375635.1:c.54+12804C>G

Variant summary

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

The NM_001375635.1(CDC42SE2):​c.54+12804C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,926 control chromosomes in the GnomAD database, including 4,302 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 (4302 hom., cov: 31)
• Consequence: CDC42SE2 NM_001375635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt
CDC42SE2	NM_001375635.1	c.54+12804C>G		intron_variant	Intron 3 of 4	ENST00000505065.2	NP_001362564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42SE2	ENST00000505065.2	c.54+12804C>G		intron_variant	Intron 3 of 4	1	NM_001375635.1	ENSP00000427421.1
CDC42SE2	ENST00000360515.7	c.54+12804C>G		intron_variant	Intron 3 of 5	1		ENSP00000353706.3
CDC42SE2	ENST00000503291.5	c.-28+12793C>G		intron_variant	Intron 3 of 5	1		ENSP00000426779.1
CDC42SE2	ENST00000395246.5	c.54+12804C>G		intron_variant	Intron 2 of 4	5		ENSP00000378667.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34868 AN: 151806 Hom.: 4295 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.230 AC: 34911 AN: 151926 Hom.: 4302 Cov.: 31 AF XY: 0.239 AC XY: 17726 AN XY: 74230

African (AFR) AF: 0.191 AC: 7905 AN: 41396

American (AMR) AF: 0.250 AC: 3821 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3470

East Asian (EAS) AF: 0.485 AC: 2510 AN: 5170

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4820

European-Finnish (FIN) AF: 0.371 AC: 3893 AN: 10504

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13775 AN: 67982

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.108 Hom.: 220

Bravo AF: 0.220

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs40396; hg19: chr5-130708044;