2-233238312-C-G

Variant names:

• chr2-233238312-C-G
• rs12471449
• ENST00000431917.5:c.-137-17790C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431917.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG16L1	ENST00000431917.5	TSL:5	c.-137-17790C>G		intron	N/A	ENSP00000397512.1

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

African (AFR) AF: 0.156 AC: 6475 AN: 41492

American (AMR) AF: 0.131 AC: 2001 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.0950 AC: 492 AN: 5178

South Asian (SAS) AF: 0.0949 AC: 457 AN: 4816

European-Finnish (FIN) AF: 0.139 AC: 1473 AN: 10584

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9145 AN: 68006

Other (OTH) AF: 0.123 AC: 260 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.82
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs12471449; hg19: chr2-234146958;