rs4663396

chr2-233283605-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030803.7(ATG16L1):c.1203+852C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 150,540 control chromosomes in the GnomAD database, including 5,678 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 0.26 (5678 hom., cov: 30)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG16L1	NM_030803.7	c.1203+852C>T		intron_variant		ENST00000392017.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG16L1	ENST00000392017.9	c.1203+852C>T		intron_variant		1	NM_030803.7	P3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 38977 AN: 150432 Hom.: 5669 Cov.: 30

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.259 AC: 39029 AN: 150540 Hom.: 5678 Cov.: 30 AF XY: 0.262 AC XY: 19211 AN XY: 73306

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.230

Alfa AF: 0.237 Hom.: 798

Bravo AF: 0.262

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.2
Dann	Benign	0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4663396; hg19: chr2-234192251;