rs2241880

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_030803.7(ATG16L1):​c.898A>C​(p.Thr300Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ATG16L1
NM_030803.7 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.448
Variant links:
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.050829947).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATG16L1NM_030803.7 linkc.898A>C p.Thr300Pro missense_variant Exon 9 of 18 ENST00000392017.9 NP_110430.5 Q676U5-1Q17RG0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATG16L1ENST00000392017.9 linkc.898A>C p.Thr300Pro missense_variant Exon 9 of 18 1 NM_030803.7 ENSP00000375872.4 Q676U5-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1459986
Hom.:
0
Cov.:
36
AF XY:
0.00
AC XY:
0
AN XY:
726372
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.059
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
1.7
DANN
Benign
0.89
DEOGEN2
Benign
0.041
.;T;T;.;T;.;.
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.082
N
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.051
T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.34
.;N;.;.;.;.;.
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-1.1
N;N;N;N;N;N;N
REVEL
Benign
0.14
Sift
Benign
0.18
T;T;T;T;.;T;T
Sift4G
Benign
0.38
T;T;T;T;T;T;T
Polyphen
0.0, 0.0020
.;B;.;B;.;B;.
Vest4
0.082
MutPred
0.20
.;Loss of phosphorylation at T300 (P = 0.0722);.;.;.;.;.;
MVP
0.74
MPC
0.74
ClinPred
0.077
T
GERP RS
-11
Varity_R
0.18
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-234183368; API