5-131324065-C-G

Variant names:

• chr5-131324065-C-G
• rs2549012
• NM_001375635.1:c.-286+7921C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001375635.1(CDC42SE2):​c.-286+7921C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

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>G		intron	N/A	NP_001362564.1	Q9NRR3
	CDC42SE2	NM_001038702.2		c.-285-35144C>G		intron	N/A	NP_001033791.1	Q9NRR3
	CDC42SE2	NM_001375633.1		c.-286+7921C>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.-286+7921C>G		intron	N/A	ENSP00000427421.1	Q9NRR3
	CDC42SE2	ENST00000360515.7	TSL:1	c.-286+7921C>G		intron	N/A	ENSP00000353706.3	Q9NRR3
	CDC42SE2	ENST00000503291.5	TSL:1	c.-378+7921C>G		intron	N/A	ENSP00000426779.1	D6REL0

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 12215

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	0.39
PhyloP100		-0.46

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;