chr2-233272910-C-A

Variant names:

• chr2-233272910-C-A
• rs2289476
• NM_030803.7:c.708-56C>A

Variant summary

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

The NM_030803.7(ATG16L1):​c.708-56C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0715 in 1,478,832 control chromosomes in the GnomAD database, including 4,823 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 0.097 (927 hom., cov: 33)
  • Exomes 𝑓: 0.069 (3896 hom.)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG16L1	NM_030803.7	c.708-56C>A		intron_variant	Intron 6 of 17	ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.708-56C>A		intron_variant	Intron 6 of 17	1	NM_030803.7	ENSP00000375872.4

Frequencies

GnomAD3 genomes AF: 0.0966 AC: 14685 AN: 152082 Hom.: 926 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0424

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0845

GnomAD4 exome AF: 0.0686 AC: 91047 AN: 1326632 Hom.: 3896 AF XY: 0.0710 AC XY: 47374 AN XY: 667552

African (AFR) AF: 0.174 AC: 5346 AN: 30668

American (AMR) AF: 0.0591 AC: 2602 AN: 43990

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 1865 AN: 25180

East Asian (EAS) AF: 0.0429 AC: 1674 AN: 38976

South Asian (SAS) AF: 0.153 AC: 12657 AN: 82936

European-Finnish (FIN) AF: 0.0772 AC: 4111 AN: 53240

Middle Eastern (MID) AF: 0.0551 AC: 304 AN: 5516

European-Non Finnish (NFE) AF: 0.0588 AC: 58201 AN: 990294

Other (OTH) AF: 0.0768 AC: 4287 AN: 55832

GnomAD4 genome AF: 0.0966 AC: 14706 AN: 152200 Hom.: 927 Cov.: 33 AF XY: 0.0987 AC XY: 7346 AN XY: 74408

African (AFR) AF: 0.172 AC: 7131 AN: 41496

American (AMR) AF: 0.0796 AC: 1217 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.0429 AC: 222 AN: 5180

South Asian (SAS) AF: 0.153 AC: 739 AN: 4824

European-Finnish (FIN) AF: 0.0818 AC: 867 AN: 10596

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0591 AC: 4019 AN: 68026

Other (OTH) AF: 0.0879 AC: 186 AN: 2116

Alfa AF: 0.0646 Hom.: 272

Bravo AF: 0.0977

Asia WGS AF: 0.123 AC: 430 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	0.58
DANN	Benign	0.67
PhyloP100		-0.11
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: rs2289476; hg19: chr2-234181556;