dbSNP rs2241879: ATG16L1:c.954+44G>A (chr2-233274822-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08

Publications

36 publications found

Variant links:

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]

ATG16L1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG16L1	NM_030803.7 link	c.954+44G>A		intron_variant	Intron 9 of 17	ENST00000392017.9	NP_110430.5	Q676U5-1Q17RG0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9 link	c.954+44G>A		intron_variant	Intron 9 of 17	1	NM_030803.7	ENSP00000375872.4		Q676U5-1

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66319

AN:

151880

Hom.:

15154

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.497

AC XY:

320436

AN XY:

644274

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

13467

26933

40400

53866

67333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13224

26448

39672

52896

66120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.436

AC:

66317

AN:

151998

Hom.:

15153

Cov.:

AF XY:

0.431

AC XY:

32025

AN XY:

74284

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1868

3737

5605

7474

9342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.077

(source)

DANN

Benign

0.65

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over