dbSNP rs78835907: ATG16L1:c.-190G>A (chr2-233210531-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000431917(ATG16L1):c.-190G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 152,480 control chromosomes in the GnomAD database, including 519 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 0.055 ( 519 hom., cov: 33)

Exomes 𝑓: 0.027 ( 0 hom. )

Consequence

ATG16L1
ENST00000431917 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000431917 link	c.-190G>A		5_prime_UTR_variant	Exon 2 of 6	5		ENSP00000397512.1		C9J8C6

Frequencies

GnomAD3 genomes

AF:

0.0551

AC:

8385

AN:

152102

Hom.:

515

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0382

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0527

Gnomad ASJ

AF:

0.0999

Gnomad EAS

AF:

0.331

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.0324

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0393

Gnomad OTH

AF:

0.0601

GnomAD4 exome

AF:

0.0269

AC:

AN:

260

Hom.:

Cov.:

AF XY:

0.0267

AC XY:

AN XY:

150

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.0119

Gnomad4 NFE exome

AF:

0.0242

Gnomad4 OTH exome

AF:

0.0238

GnomAD4 genome

AF:

0.0551

AC:

8394

AN:

152220

Hom.:

519

Cov.:

AF XY:

0.0576

AC XY:

4288

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.0382

Gnomad4 AMR

AF:

0.0526

Gnomad4 ASJ

AF:

0.0999

Gnomad4 EAS

AF:

0.331

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.0324

Gnomad4 NFE

AF:

0.0393

Gnomad4 OTH

AF:

0.0642

Alfa

AF:

0.0440

Hom.:

Bravo

AF:

0.0568

Asia WGS

AF:

0.251

AC:

871

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

2.4

DANN

Benign

0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over