5-131324065-C-A

Variant names:

• chr5-131324065-C-A
• rs2549012
• NM_001375635.1:c.-286+7921C>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.-286+7921C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 152,006 control chromosomes in the GnomAD database, including 15,181 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 0.40 (15181 hom., cov: 32)
• Consequence: CDC42SE2 NM_001375635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 4 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 = 0.563 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.-286+7921C>A		intron	N/A	NP_001362564.1	Q9NRR3
	CDC42SE2	NM_001038702.2		c.-285-35144C>A		intron	N/A	NP_001033791.1	Q9NRR3
	CDC42SE2	NM_001375633.1		c.-286+7921C>A		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.-286+7921C>A		intron	N/A	ENSP00000427421.1	Q9NRR3
	CDC42SE2	ENST00000360515.7	TSL:1	c.-286+7921C>A		intron	N/A	ENSP00000353706.3	Q9NRR3
	CDC42SE2	ENST00000503291.5	TSL:1	c.-378+7921C>A		intron	N/A	ENSP00000426779.1	D6REL0

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61450 AN: 151888 Hom.: 15187 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.0872

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.404 AC: 61433 AN: 152006 Hom.: 15181 Cov.: 32 AF XY: 0.399 AC XY: 29631 AN XY: 74308

African (AFR) AF: 0.144 AC: 5977 AN: 41488

American (AMR) AF: 0.427 AC: 6509 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3472

East Asian (EAS) AF: 0.0865 AC: 448 AN: 5180

South Asian (SAS) AF: 0.452 AC: 2179 AN: 4822

European-Finnish (FIN) AF: 0.424 AC: 4470 AN: 10534

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38562 AN: 67944

Other (OTH) AF: 0.436 AC: 921 AN: 2112

Alfa AF: 0.503 Hom.: 12215

Bravo AF: 0.389

Asia WGS AF: 0.231 AC: 802 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.21
PhyloP100		-0.46
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: rs2549012; hg19: chr5-130659758;