2-219221098-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001077198.3(ATG9A):c.2350C>T(p.Arg784Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000753 in 1,460,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
ATG9A
NM_001077198.3 missense
NM_001077198.3 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 5.13
Genes affected
ATG9A (HGNC:22408): (autophagy related 9A) Acts upstream of or within autophagosome assembly. Located in endosome; phagophore assembly site; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37150815).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATG9A | NM_001077198.3 | c.2350C>T | p.Arg784Cys | missense_variant | 14/16 | ENST00000361242.9 | NP_001070666.1 | |
ATG9A | NM_024085.5 | c.2350C>T | p.Arg784Cys | missense_variant | 13/15 | NP_076990.4 | ||
ATG9A | NR_104255.2 | n.2474C>T | non_coding_transcript_exon_variant | 14/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATG9A | ENST00000361242.9 | c.2350C>T | p.Arg784Cys | missense_variant | 14/16 | 2 | NM_001077198.3 | ENSP00000355173.4 | ||
ENSG00000284820 | ENST00000446716.5 | n.595C>T | non_coding_transcript_exon_variant | 4/22 | 2 | ENSP00000398528.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.0000203 AC: 5AN: 245708Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133666
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460786Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726594
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GnomAD4 genome Cov.: 31
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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 | Apr 05, 2024 | The c.2350C>T (p.R784C) alteration is located in exon 14 (coding exon 12) of the ATG9A gene. This alteration results from a C to T substitution at nucleotide position 2350, causing the arginine (R) at amino acid position 784 to be replaced by a cysteine (C). 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
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;.;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
B;B;B;.
Vest4
MutPred
Loss of disorder (P = 0.036);Loss of disorder (P = 0.036);Loss of disorder (P = 0.036);.;
MVP
MPC
0.30
ClinPred
T
GERP RS
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