chr3-11340731-A-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001349232.2(ATG7):c.976A>C(p.Lys326Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000717 in 1,612,870 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0036 ( 2 hom., cov: 31)
Exomes 𝑓: 0.00041 ( 7 hom. )
Consequence
ATG7
NM_001349232.2 missense
NM_001349232.2 missense
Scores
2
4
10
Clinical Significance
Conservation
PhyloP100: 8.50
Genes affected
ATG7 (HGNC:16935): (autophagy related 7) This gene encodes an E1-like activating enzyme that is essential for autophagy and cytoplasmic to vacuole transport. The encoded protein is also thought to modulate p53-dependent cell cycle pathways during prolonged metabolic stress. It has been associated with multiple functions, including axon membrane trafficking, axonal homeostasis, mitophagy, adipose differentiation, and hematopoietic stem cell maintenance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009667546).
BP6
?
Variant 3-11340731-A-C is Benign according to our data. Variant chr3-11340731-A-C is described in ClinVar as [Benign]. Clinvar id is 734811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATG7 | NM_001349232.2 | c.976A>C | p.Lys326Gln | missense_variant | 12/21 | ENST00000693202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATG7 | ENST00000693202.1 | c.976A>C | p.Lys326Gln | missense_variant | 12/21 | NM_001349232.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00364 AC: 554AN: 152078Hom.: 2 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000960 AC: 241AN: 251136Hom.: 2 AF XY: 0.000722 AC XY: 98AN XY: 135702
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GnomAD4 exome AF: 0.000413 AC: 603AN: 1460674Hom.: 7 Cov.: 30 AF XY: 0.000365 AC XY: 265AN XY: 726644
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GnomAD4 genome ? AF: 0.00364 AC: 554AN: 152196Hom.: 2 Cov.: 31 AF XY: 0.00375 AC XY: 279AN XY: 74414
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | ATG7: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.53, 0.54
.;P;P
Vest4
MVP
MPC
0.32
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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