rs12994997
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030803.7(ATG16L1):c.390-35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 1,610,478 control chromosomes in the GnomAD database, including 202,772 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 0.44 ( 15107 hom., cov: 32)
Exomes 𝑓: 0.50 ( 187665 hom. )
Consequence
ATG16L1
NM_030803.7 intron
NM_030803.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.227
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=-0.88).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATG16L1 | NM_030803.7 | c.390-35G>A | intron_variant | ENST00000392017.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATG16L1 | ENST00000392017.9 | c.390-35G>A | intron_variant | 1 | NM_030803.7 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.435 AC: 66137AN: 151902Hom.: 15106 Cov.: 32
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GnomAD3 exomes AF: 0.452 AC: 112742AN: 249188Hom.: 27300 AF XY: 0.468 AC XY: 63036AN XY: 134726
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GnomAD4 exome AF: 0.501 AC: 730868AN: 1458458Hom.: 187665 Cov.: 43 AF XY: 0.504 AC XY: 365407AN XY: 725420
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GnomAD4 genome ? AF: 0.435 AC: 66136AN: 152020Hom.: 15107 Cov.: 32 AF XY: 0.430 AC XY: 31943AN XY: 74306
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at