2-219221098-G-A

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

Scores

2
7
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.13
Variant links:
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]

Genome browser will be placed here

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
ATG9ANM_001077198.3 linkc.2350C>T p.Arg784Cys missense_variant 14/16 ENST00000361242.9 NP_001070666.1 Q7Z3C6-1A0A024R438
ATG9ANM_024085.5 linkc.2350C>T p.Arg784Cys missense_variant 13/15 NP_076990.4 Q7Z3C6-1A0A024R438
ATG9ANR_104255.2 linkn.2474C>T non_coding_transcript_exon_variant 14/16

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATG9AENST00000361242.9 linkc.2350C>T p.Arg784Cys missense_variant 14/162 NM_001077198.3 ENSP00000355173.4 Q7Z3C6-1
ENSG00000284820ENST00000446716.5 linkn.595C>T non_coding_transcript_exon_variant 4/222 ENSP00000398528.1 H7C152

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.0000203
AC:
5
AN:
245708
Hom.:
0
AF XY:
0.0000224
AC XY:
3
AN XY:
133666
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000291
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000659
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000181
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000753
AC:
11
AN:
1460786
Hom.:
0
Cov.:
31
AF XY:
0.00000688
AC XY:
5
AN XY:
726594
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.0000282
Hom.:
0
Bravo
AF:
0.00000378
ExAC
AF:
0.0000248
AC:
3
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

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 submitterclinical testingAmbry GeneticsApr 05, 2024The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Uncertain
0.042
T
BayesDel_noAF
Uncertain
0.0
CADD
Pathogenic
27
DANN
Uncertain
0.99
DEOGEN2
Benign
0.076
T;T;T;.
Eigen
Benign
0.069
Eigen_PC
Uncertain
0.27
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.91
.;.;D;D
M_CAP
Benign
0.023
T
MetaRNN
Benign
0.37
T;T;T;T
MetaSVM
Benign
-0.79
T
MutationAssessor
Benign
1.0
L;L;L;.
PrimateAI
Pathogenic
0.82
D
PROVEAN
Benign
-1.4
N;N;N;N
REVEL
Benign
0.28
Sift
Uncertain
0.0040
D;D;D;D
Sift4G
Uncertain
0.0060
D;D;D;D
Polyphen
0.029
B;B;B;.
Vest4
0.58
MutPred
0.54
Loss of disorder (P = 0.036);Loss of disorder (P = 0.036);Loss of disorder (P = 0.036);.;
MVP
0.73
MPC
0.30
ClinPred
0.40
T
GERP RS
5.3
Varity_R
0.28
gMVP
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs776035970; hg19: chr2-220085820; COSMIC: COSV54701247; COSMIC: COSV54701247; API