NM_030803.7:c.954+44G>A

Variant names:

• chr2-233274822-G-A
• rs2241879
• NM_030803.7:c.954+44G>A

Variant summary

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

The NM_030803.7(ATG16L1):​c.954+44G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 1,433,360 control chromosomes in the GnomAD database, including 175,758 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 (15153 hom., cov: 32)
  • Exomes 𝑓: 0.49 (160605 hom.)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 36 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=-0.91).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG16L1	NM_030803.7	MANE Select	c.954+44G>A		intron	N/A	NP_110430.5
	ATG16L1	NM_001363742.2		c.1005+44G>A		intron	N/A	NP_001350671.1
	ATG16L1	NM_017974.4		c.897+44G>A		intron	N/A	NP_060444.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG16L1	ENST00000392017.9	TSL:1 MANE Select	c.954+44G>A		intron	N/A	ENSP00000375872.4
	ATG16L1	ENST00000392020.8	TSL:1	c.897+44G>A		intron	N/A	ENSP00000375875.4
	ATG16L1	ENST00000347464.9	TSL:1	c.465+44G>A		intron	N/A	ENSP00000318259.6

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66319 AN: 151880 Hom.: 15154 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.443

GnomAD2 exomes AF: 0.450 AC: 108662 AN: 241340 AF XY: 0.466

Gnomad AFR exome AF: 0.323

Gnomad AMR exome AF: 0.235

Gnomad ASJ exome AF: 0.614

Gnomad EAS exome AF: 0.331

Gnomad FIN exome AF: 0.445

Gnomad NFE exome AF: 0.521

Gnomad OTH exome AF: 0.468

GnomAD4 exome AF: 0.494 AC: 632481 AN: 1281362 Hom.: 160605 Cov.: 17 AF XY: 0.497 AC XY: 320436 AN XY: 644274

African (AFR) AF: 0.314 AC: 9386 AN: 29900

American (AMR) AF: 0.250 AC: 10843 AN: 43456

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 14957 AN: 24590

East Asian (EAS) AF: 0.275 AC: 10604 AN: 38494

South Asian (SAS) AF: 0.522 AC: 42093 AN: 80686

European-Finnish (FIN) AF: 0.440 AC: 22748 AN: 51736

Middle Eastern (MID) AF: 0.528 AC: 2486 AN: 4712

European-Non Finnish (NFE) AF: 0.517 AC: 493120 AN: 953480

Other (OTH) AF: 0.483 AC: 26244 AN: 54308

GnomAD4 genome AF: 0.436 AC: 66317 AN: 151998 Hom.: 15153 Cov.: 32 AF XY: 0.431 AC XY: 32025 AN XY: 74284

African (AFR) AF: 0.322 AC: 13337 AN: 41468

American (AMR) AF: 0.353 AC: 5391 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2083 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5164

South Asian (SAS) AF: 0.510 AC: 2452 AN: 4810

European-Finnish (FIN) AF: 0.437 AC: 4617 AN: 10564

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

European-Non Finnish (NFE) AF: 0.519 AC: 35256 AN: 67950

Other (OTH) AF: 0.438 AC: 923 AN: 2108

Alfa AF: 0.491 Hom.: 53874

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	-0.91
CADD	Benign	0.077
DANN	Benign	0.65
PhyloP100		-2.1
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: rs2241879; hg19: chr2-234183468;