rs2241879

Positions:

• chr2-233274822-G-A

Variant summary

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

The ENST00000392017.9(ATG16L1):​c.954+44G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 1,433,360 control chromosomes in the GnomAD database, including 175,758 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 (15153 hom., cov: 32)
  • Exomes 𝑓: 0.49 (160605 hom.)
• Consequence: ATG16L1 ENST00000392017.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

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=-0.91).
• 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/exons	MANE	Protein	UniProt
ATG16L1	NM_030803.7	c.954+44G>A		intron_variant		ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.954+44G>A		intron_variant		1	NM_030803.7	ENSP00000375872	P3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66319 AN: 151880 Hom.: 15154 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.443

GnomAD3 exomes AF: 0.450 AC: 108662 AN: 241340 Hom.: 26007 AF XY: 0.466 AC XY: 60814 AN XY: 130526

Gnomad AFR exome AF: 0.323

Gnomad AMR exome AF: 0.235

Gnomad ASJ exome AF: 0.614

Gnomad EAS exome AF: 0.331

Gnomad SAS exome AF: 0.517

Gnomad FIN exome AF: 0.445

Gnomad NFE exome AF: 0.521

Gnomad OTH exome AF: 0.468

GnomAD4 exome AF: 0.494 AC: 632481 AN: 1281362 Hom.: 160605 Cov.: 17 AF XY: 0.497 AC XY: 320436 AN XY: 644274

Gnomad4 AFR exome AF: 0.314

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.608

Gnomad4 EAS exome AF: 0.275

Gnomad4 SAS exome AF: 0.522

Gnomad4 FIN exome AF: 0.440

Gnomad4 NFE exome AF: 0.517

Gnomad4 OTH exome AF: 0.483

GnomAD4 genome AF: 0.436 AC: 66317 AN: 151998 Hom.: 15153 Cov.: 32 AF XY: 0.431 AC XY: 32025 AN XY: 74284

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.438

Alfa AF: 0.507 Hom.: 34819

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	-0.91
CADD	Benign	0.077
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2241879; hg19: chr2-234183468;