14-55380686-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014924.5(ATG14):c.882G>A(p.Met294Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000125 in 1,595,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M294V) has been classified as Uncertain significance.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
ATG14
NM_014924.5 missense
NM_014924.5 missense
Scores
1
1
16
Clinical Significance
Conservation
PhyloP100: 4.77
Publications
0 publications found
Genes affected
ATG14 (HGNC:19962): (autophagy related 14) Enables GTPase binding activity. Involved in several processes, including macroautophagy; regulation of phosphorylation; and response to mitochondrial depolarisation. Acts upstream of or within endosome to lysosome transport. Located in autophagosome and phagophore assembly site membrane. Is extrinsic component of omegasome membrane and extrinsic component of phagophore assembly site membrane. [provided by Alliance of Genome Resources, Apr 2022]
FBXO34 (HGNC:20201): (F-box protein 34) Members of the F-box protein family, such as FBXO34, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Mar 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19205776).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014924.5. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 151902Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151902
Hom.:
Cov.:
31
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:
GnomAD4 exome AF: 6.93e-7 AC: 1AN: 1443230Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 717618 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1443230
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
717618
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32918
American (AMR)
AF:
AC:
0
AN:
41820
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25640
East Asian (EAS)
AF:
AC:
0
AN:
38998
South Asian (SAS)
AF:
AC:
0
AN:
82314
European-Finnish (FIN)
AF:
AC:
0
AN:
53166
Middle Eastern (MID)
AF:
AC:
0
AN:
5708
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1103068
Other (OTH)
AF:
AC:
0
AN:
59598
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00000658 AC: 1AN: 151902Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74184 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151902
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
74184
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41358
American (AMR)
AF:
AC:
0
AN:
15232
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5174
South Asian (SAS)
AF:
AC:
0
AN:
4812
European-Finnish (FIN)
AF:
AC:
0
AN:
10570
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67978
Other (OTH)
AF:
AC:
0
AN:
2084
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
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
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MutPred
Loss of glycosylation at P299 (P = 0.092)
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.