2-233237325-T-C

Position:

• chr2-233237325-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.233237325T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000431917.5	c.-137-18777T>C		intron_variant		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

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.528

Alfa AF: 0.568 Hom.: 18190

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13412102; hg19: chr2-234145971;