rs11605818

chr11-72835207-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 28 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG16L2	XM_005274376.6	c.1772+6223A>G		intron_variant
ATG16L2	XM_047427840.1	c.1658+6223A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG16L2	ENST00000534905.5	c.*21+6431A>G		intron_variant		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

Gnomad4 AFR AF: 0.00462

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00331

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0184

Alfa AF: 0.0233 Hom.: 68

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11605818; hg19: chr11-72546252;