rs74719094
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018036.7(ATG2B):āc.5103A>Cā(p.Arg1701Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00521 in 1,613,936 control chromosomes in the GnomAD database, including 582 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.010 ( 85 hom., cov: 32)
Exomes š: 0.0047 ( 497 hom. )
Consequence
ATG2B
NM_018036.7 missense
NM_018036.7 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: -0.541
Genes affected
ATG2B (HGNC:20187): (autophagy related 2B) This gene encodes a protein required for autophagy. The encoded protein is involved in autophagosome formation. A germline duplication of a region that includes this gene is associated with predisposition to myeloid malignancies. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002118796).
BP6
?
Variant 14-96302043-T-G is Benign according to our data. Variant chr14-96302043-T-G is described in ClinVar as [Benign]. Clinvar id is 1281030.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0879 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATG2B | NM_018036.7 | c.5103A>C | p.Arg1701Ser | missense_variant | 34/42 | ENST00000359933.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATG2B | ENST00000359933.6 | c.5103A>C | p.Arg1701Ser | missense_variant | 34/42 | 5 | NM_018036.7 | P1 | |
ATG2B | ENST00000261834.9 | n.1089A>C | non_coding_transcript_exon_variant | 7/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1575AN: 152078Hom.: 85 Cov.: 32
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GnomAD3 exomes AF: 0.0201 AC: 5050AN: 251356Hom.: 377 AF XY: 0.0151 AC XY: 2056AN XY: 135854
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GnomAD4 exome AF: 0.00467 AC: 6828AN: 1461740Hom.: 497 Cov.: 30 AF XY: 0.00391 AC XY: 2842AN XY: 727176
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GnomAD4 genome ? AF: 0.0104 AC: 1576AN: 152196Hom.: 85 Cov.: 32 AF XY: 0.0116 AC XY: 866AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
ATG2B-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 26, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Gain of disorder (P = 0.0996);
MPC
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