rs1689567146
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_152862.3(ARPC2):c.206C>T(p.Ala69Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ARPC2
NM_152862.3 missense
NM_152862.3 missense
Scores
6
12
Clinical Significance
Conservation
PhyloP100: 6.60
Publications
0 publications found
Genes affected
ARPC2 (HGNC:705): (actin related protein 2/3 complex subunit 2) This gene encodes one of seven subunits of the human Arp2/3 protein complex. The Arp2/3 protein complex has been implicated in the control of actin polymerization in cells and has been conserved through evolution. The exact role of the protein encoded by this gene, the p34 subunit, has yet to be determined. Two alternatively spliced variants have been characterized to date. Additional alternatively spliced variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.31272072).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_152862.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ARPC2 | TSL:1 MANE Select | c.206C>T | p.Ala69Val | missense | Exon 4 of 11 | ENSP00000327137.5 | O15144 | ||
| ARPC2 | TSL:1 | c.206C>T | p.Ala69Val | missense | Exon 3 of 10 | ENSP00000295685.10 | O15144 | ||
| ARPC2 | c.230C>T | p.Ala77Val | missense | Exon 5 of 12 | ENSP00000613757.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1443848Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 719242
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1443848
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
719242
African (AFR)
AF:
AC:
0
AN:
33090
American (AMR)
AF:
AC:
0
AN:
44656
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26036
East Asian (EAS)
AF:
AC:
0
AN:
39576
South Asian (SAS)
AF:
AC:
0
AN:
85854
European-Finnish (FIN)
AF:
AC:
0
AN:
53276
Middle Eastern (MID)
AF:
AC:
0
AN:
5740
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1095826
Other (OTH)
AF:
AC:
0
AN:
59794
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
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
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Loss of ubiquitination at K65 (P = 0.0997)
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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