rs6431660

Positions:

• chr2-233258588-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030803.7(ATG16L1):​c.209+2393A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,172 control chromosomes in the GnomAD database, including 14,108 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 0.41 (14108 hom., cov: 33)
• Consequence: ATG16L1 NM_030803.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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/exons	MANE	Protein	UniProt
ATG16L1	NM_030803.7	c.209+2393A>G		intron_variant		ENST00000392017.9	NP_110430.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG16L1	ENST00000392017.9	c.209+2393A>G		intron_variant		1	NM_030803.7	ENSP00000375872	P3

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62579 AN: 152056 Hom.: 14113 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.411 AC: 62563 AN: 152172 Hom.: 14108 Cov.: 33 AF XY: 0.407 AC XY: 30255 AN XY: 74390

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.419

Alfa AF: 0.402 Hom.: 2577

Bravo AF: 0.395

Asia WGS AF: 0.355 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.43
DANN	Benign	0.52

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

LitVar

Other links and lift over

dbSNP: rs6431660; hg19: chr2-234167234;