rs4663396

Variant names:

• chr2-233283605-C-T
• rs4663396
• NM_030803.7:c.1203+852C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.96).
• 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 rank	MANE	Protein	UniProt
ATG16L1	NM_030803.7	c.1203+852C>T		intron_variant	Intron 12 of 17	ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.1203+852C>T		intron_variant	Intron 12 of 17	1	NM_030803.7	ENSP00000375872.4

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

African (AFR) AF: 0.401 AC: 16416 AN: 40956

American (AMR) AF: 0.222 AC: 3347 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3460

East Asian (EAS) AF: 0.167 AC: 860 AN: 5136

South Asian (SAS) AF: 0.293 AC: 1397 AN: 4776

European-Finnish (FIN) AF: 0.244 AC: 2455 AN: 10044

Middle Eastern (MID) AF: 0.145 AC: 42 AN: 290

European-Non Finnish (NFE) AF: 0.197 AC: 13365 AN: 67796

Other (OTH) AF: 0.230 AC: 480 AN: 2084

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
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: rs4663396; hg19: chr2-234192251;