dbSNP rs3792109: ATG16L1:c.954+993G>A (chr2-233275771-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_030803.7(ATG16L1):c.954+993G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 518,942 control chromosomes in the GnomAD database, including 59,027 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 ( 14453 hom., cov: 32)

Exomes 𝑓: 0.48 ( 44574 hom. )

Consequence

ATG16L1
NM_030803.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0650

Publications

63 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:

SCARNA5 (HGNC:32561): (small Cajal body-specific RNA 5)

SCARNA5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG16L1	NM_030803.7 link	c.954+993G>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+993G>A		intron_variant	Intron 9 of 17	1	NM_030803.7	ENSP00000375872.4		Q676U5-1

Frequencies

GnomAD3 genomes

AF:

0.420

AC:

63736

AN:

151908

Hom.:

14460

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.528

Gnomad AMR

AF:

0.351

Gnomad ASJ

AF:

0.594

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.437

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.433

GnomAD2 exomes

AF:

0.450

AC:

104492

AN:

232064

AF XY:

0.467

show subpopulations

Gnomad AFR exome

AF:

0.256

Gnomad AMR exome

AF:

0.236

Gnomad ASJ exome

AF:

0.611

Gnomad EAS exome

AF:

0.333

Gnomad FIN exome

AF:

0.448

Gnomad NFE exome

AF:

0.526

Gnomad OTH exome

AF:

0.476

GnomAD4 exome

AF:

0.480

AC:

176026

AN:

366916

Hom.:

44574

Cov.:

AF XY:

0.492

AC XY:

103557

AN XY:

210390

show subpopulations

African (AFR)

AF:

0.259

AC:

2726

AN:

10510

American (AMR)

AF:

0.236

AC:

8560

AN:

36302

Ashkenazi Jewish (ASJ)

AF:

0.607

AC:

7131

AN:

11744

East Asian (EAS)

AF:

0.326

AC:

4296

AN:

13160

South Asian (SAS)

AF:

0.525

AC:

35066

AN:

66766

European-Finnish (FIN)

AF:

0.444

AC:

7514

AN:

16938

Middle Eastern (MID)

AF:

0.495

AC:

1413

AN:

2852

European-Non Finnish (NFE)

AF:

0.527

AC:

101225

AN:

192010

Other (OTH)

AF:

0.487

AC:

8095

AN:

16634

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

6137

12274

18411

24548

30685

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

632

1264

1896

2528

3160

<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:

0.419

AC:

63725

AN:

152026

Hom.:

14453

Cov.:

AF XY:

0.415

AC XY:

30832

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.257

AC:

10665

AN:

41464

American (AMR)

AF:

0.351

AC:

5357

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.594

AC:

2062

AN:

3470

East Asian (EAS)

AF:

0.314

AC:

1623

AN:

5176

South Asian (SAS)

AF:

0.508

AC:

2446

AN:

4814

European-Finnish (FIN)

AF:

0.437

AC:

4619

AN:

10564

Middle Eastern (MID)

AF:

0.507

AC:

149

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35422

AN:

67942

Other (OTH)

AF:

0.428

AC:

903

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1833

3666

5500

7333

9166

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

612

1224

1836

2448

3060

<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:

0.490

Hom.:

69359

Bravo

AF:

0.403

Asia WGS

AF:

0.356

AC:

1241

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

9.0

(source)

DANN

Benign

0.88

PhyloP100

0.065

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over