rs2289472

Variant names:

• chr2-233273594-C-T
• rs2289472
• NM_030803.7:c.795-127C>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.795-127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 859,324 control chromosomes in the GnomAD database, including 103,686 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 0.44 (15137 hom., cov: 32)
  • Exomes 𝑓: 0.49 (88549 hom.)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 18 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=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG16L1	NM_030803.7	c.795-127C>T		intron_variant	Intron 7 of 17	ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.795-127C>T		intron_variant	Intron 7 of 17	1	NM_030803.7	ENSP00000375872.4

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66286 AN: 151818 Hom.: 15138 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.441

GnomAD4 exome AF: 0.491 AC: 347211 AN: 707388 Hom.: 88549 Cov.: 9 AF XY: 0.495 AC XY: 182552 AN XY: 368774

African (AFR) AF: 0.325 AC: 5794 AN: 17804

American (AMR) AF: 0.259 AC: 7531 AN: 29054

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 10512 AN: 17238

East Asian (EAS) AF: 0.270 AC: 9474 AN: 35044

South Asian (SAS) AF: 0.524 AC: 29651 AN: 56626

European-Finnish (FIN) AF: 0.439 AC: 20814 AN: 47378

Middle Eastern (MID) AF: 0.509 AC: 2075 AN: 4078

European-Non Finnish (NFE) AF: 0.526 AC: 244634 AN: 465510

Other (OTH) AF: 0.483 AC: 16726 AN: 34656

GnomAD4 genome AF: 0.436 AC: 66283 AN: 151936 Hom.: 15137 Cov.: 32 AF XY: 0.431 AC XY: 32032 AN XY: 74294

African (AFR) AF: 0.321 AC: 13307 AN: 41402

American (AMR) AF: 0.354 AC: 5405 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2080 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1624 AN: 5178

South Asian (SAS) AF: 0.510 AC: 2457 AN: 4816

European-Finnish (FIN) AF: 0.438 AC: 4617 AN: 10548

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35248 AN: 67950

Other (OTH) AF: 0.436 AC: 916 AN: 2102

Alfa AF: 0.476 Hom.: 10701

Bravo AF: 0.422

Asia WGS AF: 0.359 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		-0.36
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: rs2289472; hg19: chr2-234182240; COSMIC: COSV61464817; COSMIC: COSV61464817;