2-233237325-T-C

Variant names:

• chr2-233237325-T-C
• rs13412102
• ENST00000431917.5:c.-137-18777T>C

Variant summary

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

The ENST00000431917.5(ATG16L1):​c.-137-18777T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,920 control chromosomes in the GnomAD database, including 22,770 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 0.54 (22770 hom., cov: 31)
• Consequence: ATG16L1 ENST00000431917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 12 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000431917.5	c.-137-18777T>C		intron_variant	Intron 2 of 5	5		ENSP00000397512.1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82549 AN: 151802 Hom.: 22768 Cov.: 31

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.544 AC: 82569 AN: 151920 Hom.: 22770 Cov.: 31 AF XY: 0.539 AC XY: 39995 AN XY: 74254

African (AFR) AF: 0.517 AC: 21408 AN: 41424

American (AMR) AF: 0.437 AC: 6668 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2252 AN: 3466

East Asian (EAS) AF: 0.365 AC: 1887 AN: 5170

South Asian (SAS) AF: 0.578 AC: 2783 AN: 4818

European-Finnish (FIN) AF: 0.534 AC: 5627 AN: 10536

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40145 AN: 67934

Other (OTH) AF: 0.528 AC: 1116 AN: 2112

Alfa AF: 0.564 Hom.: 26026

Bravo AF: 0.529

Asia WGS AF: 0.427 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.52
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs13412102; hg19: chr2-234145971;