NM_001375635.1:c.-285-20826G>A

Variant names:

• chr5-131338383-G-A
• rs4706020
• NM_001375635.1:c.-285-20826G>A

Variant summary

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

The NM_001375635.1(CDC42SE2):​c.-285-20826G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,094 control chromosomes in the GnomAD database, including 5,845 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 0.24 (5845 hom., cov: 32)
• Consequence: CDC42SE2 NM_001375635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDC42SE2	NM_001375635.1	c.-285-20826G>A		intron_variant	Intron 2 of 4	ENST00000505065.2	NP_001362564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDC42SE2	ENST00000505065.2	c.-285-20826G>A		intron_variant	Intron 2 of 4	1	NM_001375635.1	ENSP00000427421.1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36613 AN: 151976 Hom.: 5847 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.241 AC: 36605 AN: 152094 Hom.: 5845 Cov.: 32 AF XY: 0.230 AC XY: 17078 AN XY: 74344

African (AFR) AF: 0.0684 AC: 2840 AN: 41506

American (AMR) AF: 0.252 AC: 3857 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5180

South Asian (SAS) AF: 0.0911 AC: 440 AN: 4828

European-Finnish (FIN) AF: 0.258 AC: 2723 AN: 10562

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24863 AN: 67958

Other (OTH) AF: 0.274 AC: 578 AN: 2108

Alfa AF: 0.333 Hom.: 17700

Bravo AF: 0.237

Asia WGS AF: 0.0460 AC: 161 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	0.87
DANN	Benign	0.51
PhyloP100		-0.054
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: rs4706020; hg19: chr5-130674076; COSMIC: COSV64759212;