NM_030803.7:c.708-1202A>G

Variant names:

• chr2-233271764-A-G
• rs3828309
• NM_030803.7:c.708-1202A>G

Variant summary

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

The NM_030803.7(ATG16L1):​c.708-1202A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,144 control chromosomes in the GnomAD database, including 14,314 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 0.42 (14314 hom., cov: 33)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 83 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 (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.708-1202A>G		intron	N/A	NP_110430.5
	ATG16L1	NM_001363742.2		c.708-1202A>G		intron	N/A	NP_001350671.1	E7EVC7
	ATG16L1	NM_017974.4		c.708-1202A>G		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.708-1202A>G		intron	N/A	ENSP00000375872.4	Q676U5-1
	ATG16L1	ENST00000392020.8	TSL:1	c.708-1202A>G		intron	N/A	ENSP00000375875.4	Q676U5-2
	ATG16L1	ENST00000347464.9	TSL:1	c.276-1202A>G		intron	N/A	ENSP00000318259.6	Q676U5-5

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63459 AN: 152026 Hom.: 14321 Cov.: 33

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.417 AC: 63447 AN: 152144 Hom.: 14314 Cov.: 33 AF XY: 0.413 AC XY: 30696 AN XY: 74384

African (AFR) AF: 0.256 AC: 10628 AN: 41518

American (AMR) AF: 0.347 AC: 5305 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2062 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1628 AN: 5186

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4822

European-Finnish (FIN) AF: 0.436 AC: 4613 AN: 10580

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

European-Non Finnish (NFE) AF: 0.518 AC: 35230 AN: 67964

Other (OTH) AF: 0.421 AC: 890 AN: 2112

Alfa AF: 0.481 Hom.: 72635

Bravo AF: 0.401

Asia WGS AF: 0.357 AC: 1244 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	0.028
DANN	Benign	0.62
PhyloP100		-2.6
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: rs3828309; hg19: chr2-234180410;