14-57219374-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006544.4(EXOC5):c.1474A>G(p.Ile492Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000286 in 1,539,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000026 ( 0 hom. )
Consequence
EXOC5
NM_006544.4 missense
NM_006544.4 missense
Scores
5
11
Clinical Significance
Conservation
PhyloP100: 5.14
Genes affected
EXOC5 (HGNC:10696): (exocyst complex component 5) 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 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. The complex is also essential for the biogenesis of epithelial cell surface polarity. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.035819232).
BS2
?
High AC in GnomAd at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXOC5 | NM_006544.4 | c.1474A>G | p.Ile492Val | missense_variant | 14/18 | ENST00000621441.5 | |
EXOC5 | XM_005267272.4 | c.1588A>G | p.Ile530Val | missense_variant | 14/18 | ||
EXOC5 | XM_047430882.1 | c.1309A>G | p.Ile437Val | missense_variant | 14/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXOC5 | ENST00000621441.5 | c.1474A>G | p.Ile492Val | missense_variant | 14/18 | 1 | NM_006544.4 | P1 | |
EXOC5 | ENST00000554011.5 | n.1193A>G | non_coding_transcript_exon_variant | 4/8 | 1 | ||||
EXOC5 | ENST00000340918.11 | c.1279A>G | p.Ile427Val | missense_variant | 13/17 | 2 | |||
EXOC5 | ENST00000555148.5 | c.*1308A>G | 3_prime_UTR_variant, NMD_transcript_variant | 14/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000527 AC: 8AN: 151940Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
8
AN:
151940
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000785 AC: 14AN: 178368Hom.: 0 AF XY: 0.0000737 AC XY: 7AN XY: 94974
GnomAD3 exomes
AF:
AC:
14
AN:
178368
Hom.:
AF XY:
AC XY:
7
AN XY:
94974
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000260 AC: 36AN: 1387092Hom.: 0 Cov.: 24 AF XY: 0.0000233 AC XY: 16AN XY: 687326
GnomAD4 exome
AF:
AC:
36
AN:
1387092
Hom.:
Cov.:
24
AF XY:
AC XY:
16
AN XY:
687326
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74322
GnomAD4 genome
?
AF:
AC:
8
AN:
152058
Hom.:
Cov.:
32
AF XY:
AC XY:
4
AN XY:
74322
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
?
AF:
AC:
7
Asia WGS
AF:
AC:
16
AN:
3474
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.1474A>G (p.I492V) alteration is located in exon 14 (coding exon 14) of the EXOC5 gene. This alteration results from a A to G substitution at nucleotide position 1474, causing the isoleucine (I) at amino acid position 492 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
Sift4G
Benign
T;T;T
Polyphen
B;.;P
Vest4
MVP
MPC
0.49
ClinPred
T
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