chr2-233250193-C-T

Variant names:

• chr2-233250193-C-T
• rs10210302
• ENST00000431917.5:c.-137-5909C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431917.5(ATG16L1):​c.-137-5909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,074 control chromosomes in the GnomAD database, including 15,172 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 0.44 (15172 hom., cov: 33)
• Consequence: ATG16L1 ENST00000431917.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 102 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 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.-137-5909C>T		intron_variant	Intron 2 of 5	5		ENSP00000397512.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66284 AN: 151956 Hom.: 15171 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.436 AC: 66281 AN: 152074 Hom.: 15172 Cov.: 33 AF XY: 0.431 AC XY: 32003 AN XY: 74334

African (AFR) AF: 0.321 AC: 13306 AN: 41464

American (AMR) AF: 0.355 AC: 5434 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2082 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1625 AN: 5176

South Asian (SAS) AF: 0.506 AC: 2440 AN: 4818

European-Finnish (FIN) AF: 0.436 AC: 4603 AN: 10552

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35217 AN: 67990

Other (OTH) AF: 0.439 AC: 927 AN: 2114

Alfa AF: 0.486 Hom.: 60642

Bravo AF: 0.423

Asia WGS AF: 0.360 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs10210302; hg19: chr2-234158839;