2-233238312-C-G

Position:

• chr2-233238312-C-G

Variant summary

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

The ENST00000431917.5(ATG16L1):​c.-137-17790C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,142 control chromosomes in the GnomAD database, including 1,450 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 0.14 (1450 hom., cov: 32)
• Consequence: ATG16L1 ENST00000431917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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.-137-17790C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20623 AN: 152022 Hom.: 1442 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.0946

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.136 AC: 20658 AN: 152142 Hom.: 1450 Cov.: 32 AF XY: 0.135 AC XY: 10043 AN XY: 74382

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0726 Hom.: 80

Bravo AF: 0.139

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12471449; hg19: chr2-234146958;