dbSNP rs1045100: ATG16L1:n.*2306T>C (chr2-233294951-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000392021.7(ATG16L1):n.*2306T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,240 control chromosomes in the GnomAD database, including 13,157 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 0.40 ( 13127 hom., cov: 33)

Exomes 𝑓: 0.52 ( 30 hom. )

Consequence

ATG16L1
ENST00000392021.7 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.490

Publications

19 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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392021.7. 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.*601T>C	3_prime_UTR	Exon 18 of 18	NP_110430.5
ATG16L1	NM_001363742.2		c.*601T>C	3_prime_UTR	Exon 19 of 19	NP_001350671.1
ATG16L1	NM_017974.4		c.*601T>C	3_prime_UTR	Exon 17 of 17	NP_060444.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATG16L1	ENST00000392021.7	TSL:1	n.*2306T>C	non_coding_transcript_exon	Exon 18 of 18	ENSP00000375876.3
ATG16L1	ENST00000479942.5	TSL:1	n.2844T>C	non_coding_transcript_exon	Exon 17 of 17
ATG16L1	ENST00000392017.9	TSL:1 MANE Select	c.*601T>C	3_prime_UTR	Exon 18 of 18	ENSP00000375872.4

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

60978

AN:

151870

Hom.:

13132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.253

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.538

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.431

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.408

GnomAD4 exome

AF:

0.520

AC:

130

AN:

250

Hom.:

Cov.:

AF XY:

0.538

AC XY:

AN XY:

156

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.514

AC:

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.519

AC:

AN:

104

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.401

AC:

60971

AN:

151990

Hom.:

13127

Cov.:

AF XY:

0.398

AC XY:

29576

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.253

AC:

10502

AN:

41508

American (AMR)

AF:

0.331

AC:

5055

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.538

AC:

1866

AN:

3470

East Asian (EAS)

AF:

0.310

AC:

1598

AN:

5160

South Asian (SAS)

AF:

0.506

AC:

2436

AN:

4814

European-Finnish (FIN)

AF:

0.431

AC:

4545

AN:

10540

Middle Eastern (MID)

AF:

0.476

AC:

140

AN:

294

European-Non Finnish (NFE)

AF:

0.493

AC:

33509

AN:

67922

Other (OTH)

AF:

0.403

AC:

852

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1848

3695

5543

7390

9238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.451

Hom.:

33037

Bravo

AF:

0.385

Asia WGS

AF:

0.355

AC:

1237

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.6

(source)

DANN

Benign

0.61

PhyloP100

-0.49

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