chr2-233210531-G-A

Variant names:

• chr2-233210531-G-A
• rs78835907
• ENST00000431917.5:c.-190G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000431917.5	c.-190G>A		5_prime_UTR_variant	Exon 2 of 6	5		ENSP00000397512.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.0119 AC: 1 AN: 84

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0242 AC: 3 AN: 124

Other (OTH) AF: 0.0238 AC: 1 AN: 42

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

African (AFR) AF: 0.0382 AC: 1587 AN: 41534

American (AMR) AF: 0.0526 AC: 804 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0999 AC: 347 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1715 AN: 5176

South Asian (SAS) AF: 0.159 AC: 769 AN: 4826

European-Finnish (FIN) AF: 0.0324 AC: 343 AN: 10602

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0393 AC: 2672 AN: 68014

Other (OTH) AF: 0.0642 AC: 135 AN: 2102

Alfa AF: 0.0584 Hom.: 219

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
PhyloP100		-2.1
PromoterAI		-0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs78835907; hg19: chr2-234119177;