rs6431654

Variant names:

• chr2-233253123-C-T
• rs6431654
• NM_030803.7:c.115+1181C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030803.7(ATG16L1):​c.115+1181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,856 control chromosomes in the GnomAD database, including 15,224 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 (15224 hom., cov: 31)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 20 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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	c.115+1181C>T		intron_variant	Intron 1 of 17	ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.115+1181C>T		intron_variant	Intron 1 of 17	1	NM_030803.7	ENSP00000375872.4

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66436 AN: 151736 Hom.: 15223 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.447

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.437 AC: 66435 AN: 151856 Hom.: 15224 Cov.: 31 AF XY: 0.432 AC XY: 32059 AN XY: 74210

African (AFR) AF: 0.325 AC: 13436 AN: 41398

American (AMR) AF: 0.358 AC: 5460 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2085 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1626 AN: 5170

South Asian (SAS) AF: 0.509 AC: 2448 AN: 4810

European-Finnish (FIN) AF: 0.437 AC: 4597 AN: 10516

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.519 AC: 35223 AN: 67924

Other (OTH) AF: 0.442 AC: 934 AN: 2114

Alfa AF: 0.417 Hom.: 4001

Bravo AF: 0.425

Asia WGS AF: 0.360 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6431654; hg19: chr2-234161769;