GeneBe

5-131357407-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001375635.1(CDC42SE2):​c.-285-1802T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,112 control chromosomes in the GnomAD database, including 4,458 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 ( 4458 hom., cov: 32)

Consequence

CDC42SE2
NM_001375635.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.291

Publications

1 publications found
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
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 rank MANE Protein UniProt
CDC42SE2NM_001375635.1 linkc.-285-1802T>C intron_variant Intron 2 of 4 ENST00000505065.2 NP_001362564.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CDC42SE2ENST00000505065.2 linkc.-285-1802T>C intron_variant Intron 2 of 4 1 NM_001375635.1 ENSP00000427421.1 Q9NRR3

Frequencies

GnomAD3 genomes
AF:
0.232
AC:
35230
AN:
151994
Hom.:
4453
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.182
Gnomad AMI
AF:
0.269
Gnomad AMR
AF:
0.292
Gnomad ASJ
AF:
0.297
Gnomad EAS
AF:
0.486
Gnomad SAS
AF:
0.255
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.184
Gnomad NFE
AF:
0.203
Gnomad OTH
AF:
0.215
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.232
AC:
35266
AN:
152112
Hom.:
4458
Cov.:
32
AF XY:
0.242
AC XY:
17990
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.183
AC:
7586
AN:
41500
American (AMR)
AF:
0.292
AC:
4462
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.297
AC:
1031
AN:
3468
East Asian (EAS)
AF:
0.486
AC:
2512
AN:
5168
South Asian (SAS)
AF:
0.254
AC:
1228
AN:
4826
European-Finnish (FIN)
AF:
0.371
AC:
3917
AN:
10564
Middle Eastern (MID)
AF:
0.184
AC:
54
AN:
294
European-Non Finnish (NFE)
AF:
0.203
AC:
13776
AN:
67986
Other (OTH)
AF:
0.216
AC:
455
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1359
2719
4078
5438
6797
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
364
728
1092
1456
1820
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.223
Hom.:
648
Bravo
AF:
0.225
Asia WGS
AF:
0.370
AC:
1287
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.89
DANN
Benign
0.41
PhyloP100
-0.29
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

Publications

Other links and lift over

dbSNP: rs798416; hg19: chr5-130693100; API