rs193921034
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP3
The NM_001281956.2(CSMD2):c.7808G>T(p.Arg2603Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CSMD2
NM_001281956.2 missense
NM_001281956.2 missense
Scores
2
9
7
Clinical Significance
Conservation
PhyloP100: 6.16
Publications
4 publications found
Genes affected
CSMD2 (HGNC:19290): (CUB and Sushi multiple domains 2) The protein encoded by this gene is thought to be involved in the control of complement cascade of the immune system. Defects in this gene have been associated with schizophrenia. This gene may act as a tumor suppressor for colorectal cancer. [provided by RefSeq, Jan 2020]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.745
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001281956.2. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CSMD2 | TSL:1 MANE Select | c.7808G>T | p.Arg2603Leu | missense | Exon 51 of 71 | ENSP00000362479.4 | Q7Z408-4 | ||
| CSMD2 | TSL:1 | c.7814G>T | p.Arg2605Leu | missense | Exon 52 of 70 | ENSP00000362486.3 | Q7Z408-1 | ||
| CSMD2 | TSL:5 | c.7688G>T | p.Arg2563Leu | missense | Exon 51 of 71 | ENSP00000483463.1 | A0A087X0K4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1419668Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 702006
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1419668
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
702006
African (AFR)
AF:
AC:
0
AN:
32878
American (AMR)
AF:
AC:
0
AN:
43166
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25452
East Asian (EAS)
AF:
AC:
0
AN:
38724
South Asian (SAS)
AF:
AC:
0
AN:
78920
European-Finnish (FIN)
AF:
AC:
0
AN:
52610
Middle Eastern (MID)
AF:
AC:
0
AN:
5518
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1084124
Other (OTH)
AF:
AC:
0
AN:
58276
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
1
-
Prostate cancer (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Loss of disorder (P = 0.1146)
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.