GeneBe

rs773533718

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015104.3(ATG2A):​c.5614G>T​(p.Val1872Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1872M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

ATG2A
NM_015104.3 missense

Scores

1
9
8

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Publications

0 publications found
Variant links:
Genes affected
ATG2A (HGNC:29028): (autophagy related 2A) Predicted to enable phosphatidylinositol-3-phosphate binding activity. Involved in autophagosome assembly. Predicted to be located in endoplasmic reticulum membrane; lipid droplet; and phagophore assembly site membrane. Predicted to be active in phagophore assembly site. Predicted to be extrinsic component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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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_015104.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ATG2A
NM_015104.3
MANE Select
c.5614G>Tp.Val1872Leu
missense
Exon 41 of 41NP_055919.2Q2TAZ0-1
ATG2A
NM_001367972.1
c.5596G>Tp.Val1866Leu
missense
Exon 41 of 41NP_001354901.1
ATG2A
NM_001367971.1
c.5590G>Tp.Val1864Leu
missense
Exon 41 of 41NP_001354900.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ATG2A
ENST00000377264.8
TSL:1 MANE Select
c.5614G>Tp.Val1872Leu
missense
Exon 41 of 41ENSP00000366475.3Q2TAZ0-1
ATG2A
ENST00000879824.1
c.5596G>Tp.Val1866Leu
missense
Exon 41 of 41ENSP00000549883.1
ATG2A
ENST00000879823.1
c.5590G>Tp.Val1864Leu
missense
Exon 41 of 41ENSP00000549882.1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD2 exomes
AF:
0.00000404
AC:
1
AN:
247556
AF XY:
0.00
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000903
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.82
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.40
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.050
T
Eigen
Uncertain
0.44
Eigen_PC
Uncertain
0.34
FATHMM_MKL
Uncertain
0.84
D
LIST_S2
Uncertain
0.97
D
M_CAP
Benign
0.032
D
MetaRNN
Uncertain
0.44
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.6
M
PhyloP100
1.5
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
-2.2
N
REVEL
Benign
0.19
Sift
Uncertain
0.022
D
Sift4G
Benign
0.11
T
Polyphen
1.0
D
Vest4
0.51
MutPred
0.56
Loss of catalytic residue at V1872 (P = 0.1104)
MVP
0.33
MPC
1.2
ClinPred
0.92
D
GERP RS
3.8
Varity_R
0.37
gMVP
0.92
Mutation Taster
=67/33
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs773533718; hg19: chr11-64662648; API