rs778884699
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_153634.3(CPNE8):c.311G>A(p.Ser104Asn) variant causes a missense change involving the alteration of a 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: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CPNE8
NM_153634.3 missense
NM_153634.3 missense
Scores
2
8
8
Clinical Significance
Conservation
PhyloP100: 7.40
Publications
1 publications found
Genes affected
CPNE8 (HGNC:23498): (copine 8) Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene is one of several genes that encode a calcium-dependent protein containing two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. [provided by RefSeq, Jul 2008]
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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_153634.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| CPNE8 | TSL:1 MANE Select | c.311G>A | p.Ser104Asn | missense | Exon 5 of 20 | ENSP00000329748.5 | Q86YQ8-1 | ||
| CPNE8 | TSL:2 | c.275G>A | p.Ser92Asn | missense | Exon 5 of 20 | ENSP00000353633.3 | E7ENV7 | ||
| CPNE8 | c.311G>A | p.Ser104Asn | missense | Exon 5 of 20 | ENSP00000532850.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000415 AC: 1AN: 240990 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
240990
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1427932Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 710128
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1427932
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
710128
African (AFR)
AF:
AC:
0
AN:
32818
American (AMR)
AF:
AC:
0
AN:
42436
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25130
East Asian (EAS)
AF:
AC:
0
AN:
39204
South Asian (SAS)
AF:
AC:
0
AN:
82784
European-Finnish (FIN)
AF:
AC:
0
AN:
52340
Middle Eastern (MID)
AF:
AC:
0
AN:
5622
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1088776
Other (OTH)
AF:
AC:
0
AN:
58822
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ExAC
AF:
AC:
1
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
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of phosphorylation at S104 (P = 0.0506)
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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