Genetic Variant ATG16L1:c.795-127C>T (chr2-233273594-C-T) – 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.795-127C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 859,324 control chromosomes in the GnomAD database, including 103,686 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 ( 15137 hom., cov: 32)

Exomes 𝑓: 0.49 ( 88549 hom. )

Consequence

ATG16L1
NM_030803.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.356

Publications

18 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:

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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=-0.62).

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATG16L1	NM_030803.7	MANE Select	c.795-127C>T	intron	N/A	NP_110430.5
ATG16L1	NM_001363742.2		c.795-127C>T	intron	N/A	NP_001350671.1
ATG16L1	NM_017974.4		c.794+542C>T	intron	N/A	NP_060444.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATG16L1	ENST00000392017.9	TSL:1 MANE Select	c.795-127C>T	intron	N/A	ENSP00000375872.4
ATG16L1	ENST00000392020.8	TSL:1	c.794+542C>T	intron	N/A	ENSP00000375875.4
ATG16L1	ENST00000347464.9	TSL:1	c.362+542C>T	intron	N/A	ENSP00000318259.6

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66286

AN:

151818

Hom.:

15138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.355

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.510

Gnomad FIN

AF:

0.438

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.441

GnomAD4 exome

AF:

0.491

AC:

347211

AN:

707388

Hom.:

88549

Cov.:

AF XY:

0.495

AC XY:

182552

AN XY:

368774

show subpopulations

African (AFR)

AF:

0.325

AC:

5794

AN:

17804

American (AMR)

AF:

0.259

AC:

7531

AN:

29054

Ashkenazi Jewish (ASJ)

AF:

0.610

AC:

10512

AN:

17238

East Asian (EAS)

AF:

0.270

AC:

9474

AN:

35044

South Asian (SAS)

AF:

0.524

AC:

29651

AN:

56626

European-Finnish (FIN)

AF:

0.439

AC:

20814

AN:

47378

Middle Eastern (MID)

AF:

0.509

AC:

2075

AN:

4078

European-Non Finnish (NFE)

AF:

0.526

AC:

244634

AN:

465510

Other (OTH)

AF:

0.483

AC:

16726

AN:

34656

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

8387

16775

25162

33550

41937

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4074

8148

12222

16296

20370

<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:

66283

AN:

151936

Hom.:

15137

Cov.:

AF XY:

0.431

AC XY:

32032

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.321

AC:

13307

AN:

41402

American (AMR)

AF:

0.354

AC:

5405

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

2080

AN:

3468

East Asian (EAS)

AF:

0.314

AC:

1624

AN:

5178

South Asian (SAS)

AF:

0.510

AC:

2457

AN:

4816

European-Finnish (FIN)

AF:

0.438

AC:

4617

AN:

10548

Middle Eastern (MID)

AF:

0.514

AC:

151

AN:

294

European-Non Finnish (NFE)

AF:

0.519

AC:

35248

AN:

67950

Other (OTH)

AF:

0.436

AC:

916

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1834

3669

5503

7338

9172

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:

0.476

Hom.:

10701

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

-0.62

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

-0.36

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over