2-233273202-C-T

Variant names:

• chr2-233273202-C-T
• rs2289474
• NM_030803.7:c.794+150C>T

Variant summary

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

The NM_030803.7(ATG16L1):​c.794+150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 617,772 control chromosomes in the GnomAD database, including 72,850 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 (15149 hom., cov: 32)
  • Exomes 𝑓: 0.49 (57701 hom.)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 15 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030803.7. 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
	ATG16L1	NM_030803.7	MANE Select	c.794+150C>T		intron	N/A	NP_110430.5
	ATG16L1	NM_001363742.2		c.794+150C>T		intron	N/A	NP_001350671.1	E7EVC7
	ATG16L1	NM_017974.4		c.794+150C>T		intron	N/A	NP_060444.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG16L1	ENST00000392017.9	TSL:1 MANE Select	c.794+150C>T		intron	N/A	ENSP00000375872.4	Q676U5-1
	ATG16L1	ENST00000392020.8	TSL:1	c.794+150C>T		intron	N/A	ENSP00000375875.4	Q676U5-2
	ATG16L1	ENST00000347464.9	TSL:1	c.362+150C>T		intron	N/A	ENSP00000318259.6	Q676U5-5

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66318 AN: 151934 Hom.: 15150 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.442

GnomAD4 exome AF: 0.488 AC: 227363 AN: 465720 Hom.: 57701 Cov.: 5 AF XY: 0.493 AC XY: 120915 AN XY: 245190

African (AFR) AF: 0.329 AC: 4149 AN: 12614

American (AMR) AF: 0.298 AC: 5552 AN: 18616

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 8402 AN: 13772

East Asian (EAS) AF: 0.266 AC: 8149 AN: 30610

South Asian (SAS) AF: 0.527 AC: 23684 AN: 44942

European-Finnish (FIN) AF: 0.441 AC: 17877 AN: 40534

Middle Eastern (MID) AF: 0.563 AC: 1113 AN: 1976

European-Non Finnish (NFE) AF: 0.527 AC: 145846 AN: 276564

Other (OTH) AF: 0.483 AC: 12591 AN: 26092

GnomAD4 genome AF: 0.436 AC: 66315 AN: 152052 Hom.: 15149 Cov.: 32 AF XY: 0.431 AC XY: 32028 AN XY: 74328

African (AFR) AF: 0.322 AC: 13355 AN: 41496

American (AMR) AF: 0.354 AC: 5399 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1625 AN: 5174

South Asian (SAS) AF: 0.509 AC: 2447 AN: 4806

European-Finnish (FIN) AF: 0.437 AC: 4620 AN: 10566

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35235 AN: 67960

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.490 Hom.: 23924

Bravo AF: 0.422

Asia WGS AF: 0.359 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2289474; hg19: chr2-234181848;