5-131357147-C-G

Variant names:

• chr5-131357147-C-G
• rs3756295
• NM_001375635.1:c.-285-2062C>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.-285-2062C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,076 control chromosomes in the GnomAD database, including 17,233 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 0.43 (17233 hom., cov: 32)
• Consequence: CDC42SE2 NM_001375635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375635.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42SE2	NM_001375635.1	MANE Select	c.-285-2062C>G		intron	N/A	NP_001362564.1	Q9NRR3
	CDC42SE2	NM_001038702.2		c.-285-2062C>G		intron	N/A	NP_001033791.1	Q9NRR3
	CDC42SE2	NM_001375633.1		c.-285-2062C>G		intron	N/A	NP_001362562.1	Q9NRR3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDC42SE2	ENST00000505065.2	TSL:1 MANE Select	c.-285-2062C>G		intron	N/A	ENSP00000427421.1	Q9NRR3
	CDC42SE2	ENST00000360515.7	TSL:1	c.-285-2062C>G		intron	N/A	ENSP00000353706.3	Q9NRR3
	CDC42SE2	ENST00000503291.5	TSL:1	c.-377-2062C>G		intron	N/A	ENSP00000426779.1	D6REL0

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65283 AN: 151958 Hom.: 17233 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.429 AC: 65286 AN: 152076 Hom.: 17233 Cov.: 32 AF XY: 0.427 AC XY: 31745 AN XY: 74348

African (AFR) AF: 0.114 AC: 4718 AN: 41476

American (AMR) AF: 0.486 AC: 7430 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2076 AN: 5176

South Asian (SAS) AF: 0.523 AC: 2519 AN: 4816

European-Finnish (FIN) AF: 0.441 AC: 4662 AN: 10562

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40397 AN: 67976

Other (OTH) AF: 0.475 AC: 1004 AN: 2114

Alfa AF: 0.482 Hom.: 2396

Bravo AF: 0.418

Asia WGS AF: 0.408 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.68
PhyloP100		-1.0
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: rs3756295; hg19: chr5-130692840;