rs773533718

Variant summary

Our verdict is Uncertain significance. Variant got 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 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
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53
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 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 rank MANE Protein UniProt
ATG2ANM_015104.3 linkc.5614G>T p.Val1872Leu missense_variant Exon 41 of 41 ENST00000377264.8 NP_055919.2 Q2TAZ0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATG2AENST00000377264.8 linkc.5614G>T p.Val1872Leu missense_variant Exon 41 of 41 1 NM_015104.3 ENSP00000366475.3 Q2TAZ0-1
ATG2AENST00000418259.5 linkc.5023G>T p.Val1675Leu missense_variant Exon 37 of 37 5 ENSP00000413716.1 H7C3T2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000404
AC:
1
AN:
247556
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
134204
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 SAS 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 v4.3

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;D
M_CAP
Benign
0.032
D
MetaRNN
Uncertain
0.44
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.6
M;.
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
-2.2
N;.
REVEL
Benign
0.19
Sift
Uncertain
0.022
D;.
Sift4G
Benign
0.11
T;D
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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs773533718; hg19: chr11-64662648; API