rs2241880
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030803.7(ATG16L1):āc.898A>Gā(p.Thr300Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 1,609,114 control chromosomes in the GnomAD database, including 203,415 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.44 ( 15195 hom., cov: 32)
Exomes š: 0.50 ( 188220 hom. )
Consequence
ATG16L1
NM_030803.7 missense
NM_030803.7 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: -0.448
Genes affected
ATG16L1 (HGNC:21498): (autophagy related 16 like 1) The protein encoded by this gene is part of a large protein complex that is necessary for autophagy, the major process by which intracellular components are targeted to lysosomes for degradation. Defects in this gene are a cause of susceptibility to inflammatory bowel disease type 10 (IBD10). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.8645105E-5).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATG16L1 | NM_030803.7 | c.898A>G | p.Thr300Ala | missense_variant | 9/18 | ENST00000392017.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATG16L1 | ENST00000392017.9 | c.898A>G | p.Thr300Ala | missense_variant | 9/18 | 1 | NM_030803.7 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.438 AC: 66455AN: 151798Hom.: 15197 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.453 AC: 113606AN: 250652Hom.: 27569 AF XY: 0.469 AC XY: 63500AN XY: 135462
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GnomAD4 exome AF: 0.502 AC: 730915AN: 1457198Hom.: 188220 Cov.: 36 AF XY: 0.504 AC XY: 365648AN XY: 725132
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GnomAD4 genome ? AF: 0.437 AC: 66454AN: 151916Hom.: 15195 Cov.: 32 AF XY: 0.432 AC XY: 32071AN XY: 74208
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1942
ALSPAC
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2005
ESP6500AA
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1428
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ExAC
?
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ClinVar
Significance: Benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 24, 2015 | - - |
ATG16L1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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). - |
Inflammatory bowel disease 10, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Feb 27, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;.;T;T
Sift4G
Benign
T;T;T;T;T;T;T
Polyphen
0.0, 0.0010
.;B;.;B;.;B;.
Vest4
MPC
0.56
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