Variant chr5-131372351-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.524

Variant links:

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]

CDC42SE2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CDC42SE2	NM_001375635.1 link	c.54+12804C>G		intron_variant		ENST00000505065.2	NP_001362564.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CDC42SE2	ENST00000505065.2 link	c.54+12804C>G	intron_variant	1	NM_001375635.1	ENSP00000427421.1	Q9NRR3
CDC42SE2	ENST00000360515.7 link	c.54+12804C>G	intron_variant	1		ENSP00000353706.3	Q9NRR3
CDC42SE2	ENST00000503291.5 link	c.-28+12793C>G	intron_variant	1		ENSP00000426779.1	D6REL0
CDC42SE2	ENST00000395246.5 link	c.54+12804C>G	intron_variant	5		ENSP00000378667.1	Q9NRR3

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34868

AN:

151806

Hom.:

4295

Cov.:

show subpopulations

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.:

AF XY:

0.239

AC XY:

17726

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.191

Gnomad4 AMR

AF:

0.250

Gnomad4 ASJ

AF:

0.297

Gnomad4 EAS

AF:

0.485

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.371

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.212

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

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over