11-72824825-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033388.2(ATG16L2):c.979C>T(p.Arg327Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,595,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033388.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATG16L2 | NM_033388.2 | c.979C>T | p.Arg327Trp | missense_variant | 9/18 | ENST00000321297.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATG16L2 | ENST00000321297.10 | c.979C>T | p.Arg327Trp | missense_variant | 9/18 | 1 | NM_033388.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000779 AC: 18AN: 231172Hom.: 0 AF XY: 0.0000483 AC XY: 6AN XY: 124222
GnomAD4 exome AF: 0.0000291 AC: 42AN: 1443024Hom.: 0 Cov.: 30 AF XY: 0.0000363 AC XY: 26AN XY: 716564
GnomAD4 genome ? AF: 0.000282 AC: 43AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.979C>T (p.R327W) alteration is located in exon 9 (coding exon 9) of the ATG16L2 gene. This alteration results from a C to T substitution at nucleotide position 979, causing the arginine (R) at amino acid position 327 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at