rs13005285

Positions:

• chr2-233286311-T-G

Variant summary

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

The NM_030803.7(ATG16L1):​c.1204-3543T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,026 control chromosomes in the GnomAD database, including 24,870 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 0.56 (24870 hom., cov: 31)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG16L1	NM_030803.7	c.1204-3543T>G		intron_variant		ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.1204-3543T>G		intron_variant		1	NM_030803.7	ENSP00000375872	P3

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84897 AN: 151908 Hom.: 24865 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.559 AC: 84908 AN: 152026 Hom.: 24870 Cov.: 31 AF XY: 0.556 AC XY: 41317 AN XY: 74310

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.565

Alfa AF: 0.628 Hom.: 15355

Bravo AF: 0.541

Asia WGS AF: 0.490 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.76

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: rs13005285; hg19: chr2-234194957;