GeneBe

5-131358030-T-G

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.-285-1179T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,128 control chromosomes in the GnomAD database, including 4,308 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 ( 4308 hom., cov: 32)

Consequence

CDC42SE2
NM_001375635.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.462

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=-0.85).
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.-285-1179T>G 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.-285-1179T>G intron_variant Intron 2 of 4 1 NM_001375635.1 ENSP00000427421.1 Q9NRR3

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34312
AN:
152010
Hom.:
4304
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.269
Gnomad AMR
AF:
0.289
Gnomad ASJ
AF:
0.297
Gnomad EAS
AF:
0.485
Gnomad SAS
AF:
0.255
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.184
Gnomad NFE
AF:
0.203
Gnomad OTH
AF:
0.212
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.226
AC:
34345
AN:
152128
Hom.:
4308
Cov.:
32
AF XY:
0.236
AC XY:
17559
AN XY:
74354
show subpopulations
African (AFR)
AF:
0.162
AC:
6712
AN:
41514
American (AMR)
AF:
0.290
AC:
4424
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.297
AC:
1031
AN:
3468
East Asian (EAS)
AF:
0.485
AC:
2505
AN:
5160
South Asian (SAS)
AF:
0.255
AC:
1228
AN:
4822
European-Finnish (FIN)
AF:
0.371
AC:
3922
AN:
10568
Middle Eastern (MID)
AF:
0.184
AC:
54
AN:
294
European-Non Finnish (NFE)
AF:
0.203
AC:
13773
AN:
68000
Other (OTH)
AF:
0.213
AC:
451
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1329
2657
3986
5314
6643
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
354
708
1062
1416
1770
<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:
0.154
Hom.:
375
Bravo
AF:
0.218
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
-0.85
CADD
Benign
2.6
DANN
Benign
0.67
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

Publications

Other links and lift over

dbSNP: rs798415; hg19: chr5-130693723; API