rs3792106

Variant names:

• chr2-233282094-T-C
• rs3792106
• NM_030803.7:c.1132-588T>C

Variant summary

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

The NM_030803.7(ATG16L1):​c.1132-588T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,004 control chromosomes in the GnomAD database, including 22,252 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 (22252 hom., cov: 32)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 35 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 (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG16L1	NM_030803.7	c.1132-588T>C		intron_variant	Intron 11 of 17	ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.1132-588T>C		intron_variant	Intron 11 of 17	1	NM_030803.7	ENSP00000375872.4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81420 AN: 151886 Hom.: 22250 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.536 AC: 81438 AN: 152004 Hom.: 22252 Cov.: 32 AF XY: 0.533 AC XY: 39628 AN XY: 74282

African (AFR) AF: 0.493 AC: 20413 AN: 41426

American (AMR) AF: 0.434 AC: 6628 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2366 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1874 AN: 5168

South Asian (SAS) AF: 0.665 AC: 3208 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5647 AN: 10546

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39517 AN: 67978

Other (OTH) AF: 0.524 AC: 1102 AN: 2102

Alfa AF: 0.568 Hom.: 35712

Bravo AF: 0.521

Asia WGS AF: 0.490 AC: 1710 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	1.3
DANN	Benign	0.54
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3792106; hg19: chr2-234190740;