rs1045100

chr2-233294951-T-C

Variant summary

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

The NM_030803.7(ATG16L1):c.*601T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,240 control chromosomes in the GnomAD database, including 13,157 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 0.40 (13127 hom., cov: 33)
  • Exomes 𝑓: 0.52 (30 hom.)
• Consequence: ATG16L1 NM_030803.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG16L1	NM_030803.7	c.*601T>C		3_prime_UTR_variant	18/18	ENST00000392017.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG16L1	ENST00000392017.9	c.*601T>C		3_prime_UTR_variant	18/18	1	NM_030803.7	P3

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60978 AN: 151870 Hom.: 13132 Cov.: 33

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.408

GnomAD4 exome AF: 0.520 AC: 130 AN: 250 Hom.: 30 Cov.: 0 AF XY: 0.538 AC XY: 84 AN XY: 156

Gnomad4 EAS exome AF: 0.514

Gnomad4 FIN exome AF: 0.519

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.401 AC: 60971 AN: 151990 Hom.: 13127 Cov.: 33 AF XY: 0.398 AC XY: 29576 AN XY: 74294

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.403

Alfa AF: 0.478 Hom.: 22370

Bravo AF: 0.385

Asia WGS AF: 0.355 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.6
Dann	Benign	0.61

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: rs1045100; hg19: chr2-234203597;