19-7605408-A-G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_020902.2(CAMSAP3):c.331A>G(p.Arg111Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CAMSAP3
NM_020902.2 missense
NM_020902.2 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 2.63
Publications
0 publications found
Genes affected
CAMSAP3 (HGNC:29307): (calmodulin regulated spectrin associated protein family member 3) Enables actin filament binding activity and microtubule minus-end binding activity. Involved in several processes, including microtubule cytoskeleton organization; regulation of organelle organization; and zonula adherens maintenance. Located in cytoplasm; nucleoplasm; and zonula adherens. Colocalizes with centrosome and microtubule minus-end. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020902.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| CAMSAP3 | TSL:2 MANE Select | c.331A>G | p.Arg111Gly | missense | Exon 2 of 17 | ENSP00000160298.3 | Q9P1Y5-1 | ||
| CAMSAP3 | TSL:1 | c.331A>G | p.Arg111Gly | missense | Exon 2 of 19 | ENSP00000416797.1 | Q9P1Y5-2 | ||
| CAMSAP3 | c.331A>G | p.Arg111Gly | missense | Exon 2 of 17 | ENSP00000600567.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
30
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1360752Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 668316
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1360752
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
668316
African (AFR)
AF:
AC:
0
AN:
29482
American (AMR)
AF:
AC:
0
AN:
31264
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21366
East Asian (EAS)
AF:
AC:
0
AN:
35324
South Asian (SAS)
AF:
AC:
0
AN:
74658
European-Finnish (FIN)
AF:
AC:
0
AN:
50574
Middle Eastern (MID)
AF:
AC:
0
AN:
5298
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1057122
Other (OTH)
AF:
AC:
0
AN:
55664
GnomAD4 genome
GnomAD4 genome
Cov.:
30
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of stability (P = 0.008)
MVP
MPC
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
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