rs78835907

chr2-233210531-G-A

Variant summary

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

The ENST00000431917.5(ATG16L1):c.-190G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 152,480 control chromosomes in the GnomAD database, including 519 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 0.055 (519 hom., cov: 33)
  • Exomes 𝑓: 0.027 (0 hom.)
• Consequence: ATG16L1 ENST00000431917.5 5_prime_UTR
• 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 (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG16L1	ENST00000431917.5	c.-190G>A		5_prime_UTR_variant	2/6	5

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 8385 AN: 152102 Hom.: 515 Cov.: 33

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0324

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0393

Gnomad OTH AF: 0.0601

GnomAD4 exome AF: 0.0269 AC: 7 AN: 260 Hom.: 0 Cov.: 0 AF XY: 0.0267 AC XY: 4 AN XY: 150

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.0119

Gnomad4 NFE exome AF: 0.0242

Gnomad4 OTH exome AF: 0.0238

GnomAD4 genome AF: 0.0551 AC: 8394 AN: 152220 Hom.: 519 Cov.: 33 AF XY: 0.0576 AC XY: 4288 AN XY: 74426

Gnomad4 AFR AF: 0.0382

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0999

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0324

Gnomad4 NFE AF: 0.0393

Gnomad4 OTH AF: 0.0642

Alfa AF: 0.0440 Hom.: 30

Bravo AF: 0.0568

Asia WGS AF: 0.251 AC: 871 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	2.4
Dann	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs78835907; hg19: chr2-234119177;