chr2-233234598-A-G

Variant names:

• chr2-233234598-A-G
• rs7563345
• ENST00000431917.5:c.-137-21504A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431917.5(ATG16L1):​c.-137-21504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,040 control chromosomes in the GnomAD database, including 30,434 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 0.63 (30434 hom., cov: 32)
• Consequence: ATG16L1 ENST00000431917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431917.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG16L1	ENST00000431917.5	TSL:5	c.-137-21504A>G		intron	N/A	ENSP00000397512.1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95787 AN: 151922 Hom.: 30410 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.630 AC: 95845 AN: 152040 Hom.: 30434 Cov.: 32 AF XY: 0.623 AC XY: 46273 AN XY: 74326

African (AFR) AF: 0.661 AC: 27427 AN: 41476

American (AMR) AF: 0.516 AC: 7868 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2326 AN: 3466

East Asian (EAS) AF: 0.452 AC: 2334 AN: 5168

South Asian (SAS) AF: 0.638 AC: 3075 AN: 4816

European-Finnish (FIN) AF: 0.570 AC: 6012 AN: 10554

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44776 AN: 67986

Other (OTH) AF: 0.603 AC: 1274 AN: 2114

Alfa AF: 0.645 Hom.: 117205

Bravo AF: 0.626

Asia WGS AF: 0.497 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.69
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7563345; hg19: chr2-234143244;