rs11605818

Variant names:

• chr11-72835207-A-G
• rs11605818
• ENST00000534905.5:c.*21+6431A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000534905.5(ATG16L2):​c.*21+6431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0165 in 152,360 control chromosomes in the GnomAD database, including 28 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 0.017 (28 hom., cov: 32)
• Consequence: ATG16L2 ENST00000534905.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 3 publications found

Genes affected

ATG16L2 (HGNC:25464): (autophagy related 16 like 2) Predicted to be involved in autophagosome assembly and negative stranded viral RNA replication. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0165 (2518/152360) while in subpopulation NFE AF = 0.0265 (1802/68028). AF 95% confidence interval is 0.0255. There are 28 homozygotes in GnomAd4. There are 1154 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG16L2	XM_005274376.6	c.1772+6223A>G		intron_variant	Intron 17 of 17		XP_005274433.1
ATG16L2	XM_047427840.1	c.1658+6223A>G		intron_variant	Intron 16 of 16		XP_047283796.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG16L2	ENST00000534905.5	c.*21+6431A>G		intron_variant	Intron 5 of 5	1		ENSP00000441189.1

Frequencies

GnomAD3 genomes AF: 0.0165 AC: 2516 AN: 152242 Hom.: 28 Cov.: 32

Gnomad AFR AF: 0.00463

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0165 AC: 2518 AN: 152360 Hom.: 28 Cov.: 32 AF XY: 0.0155 AC XY: 1154 AN XY: 74504

African (AFR) AF: 0.00462 AC: 192 AN: 41580

American (AMR) AF: 0.0189 AC: 289 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00230 AC: 8 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5196

South Asian (SAS) AF: 0.00331 AC: 16 AN: 4832

European-Finnish (FIN) AF: 0.0133 AC: 141 AN: 10626

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0265 AC: 1802 AN: 68028

Other (OTH) AF: 0.0184 AC: 39 AN: 2116

Alfa AF: 0.0216 Hom.: 84

Bravo AF: 0.0175

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.27
PhyloP100		0.024
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11605818; hg19: chr11-72546252;