chr4-55871918-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001024924.2(EXOC1):c.1034G>A(p.Arg345Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,596 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000066 ( 0 hom. )
Consequence
EXOC1
NM_001024924.2 missense
NM_001024924.2 missense
Scores
1
2
15
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.59
Genes affected
EXOC1 (HGNC:30380): (exocyst complex component 1) The protein encoded by this gene is a component of the exocyst complex, a multiple protein complex essential for targeting exocytic vesicles to specific docking sites on the plasma membrane. Though best characterized in yeast, the component proteins and functions of the exocyst complex have been demonstrated to be highly conserved in higher eukaryotes. At least eight components of the exocyst complex, including this protein, are found to interact with the actin cytoskeletal remodeling and vesicle transport machinery. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOC1 | NM_001024924.2 | c.1034G>A | p.Arg345Gln | missense_variant | 8/19 | ENST00000381295.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOC1 | ENST00000381295.7 | c.1034G>A | p.Arg345Gln | missense_variant | 8/19 | 1 | NM_001024924.2 | A1 | |
EXOC1 | ENST00000346134.11 | c.1034G>A | p.Arg345Gln | missense_variant | 8/19 | 2 | A1 | ||
EXOC1 | ENST00000349598.6 | c.1034G>A | p.Arg345Gln | missense_variant | 8/18 | 2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152068Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251024Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135650
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GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461528Hom.: 0 Cov.: 30 AF XY: 0.0000756 AC XY: 55AN XY: 727044
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GnomAD4 genome AF: 0.0000329 AC: 5AN: 152068Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74296
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at