rs78835907
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000431917.5(ATG16L1):c.-190G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 152,480 control chromosomes in the GnomAD database, including 519 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.055 ( 519 hom., cov: 33)
Exomes 𝑓: 0.027 ( 0 hom. )
Consequence
ATG16L1
ENST00000431917.5 5_prime_UTR
ENST00000431917.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.08
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 (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATG16L1 | ENST00000431917.5 | c.-190G>A | 5_prime_UTR_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0551 AC: 8385AN: 152102Hom.: 515 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.0269 AC: 7AN: 260Hom.: 0 Cov.: 0 AF XY: 0.0267 AC XY: 4AN XY: 150
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GnomAD4 genome ? AF: 0.0551 AC: 8394AN: 152220Hom.: 519 Cov.: 33 AF XY: 0.0576 AC XY: 4288AN XY: 74426
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at