rs4752926

Positions:

• chr11-46671320-C-T

Variant summary

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

The NM_001346311.2(ATG13):​c.1576-935C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,152 control chromosomes in the GnomAD database, including 20,158 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 0.47 (20158 hom., cov: 33)
• Consequence: ATG13 NM_001346311.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

Genes affected

ATG13 (HGNC:29091): (autophagy related 13) The protein encoded by this gene is an autophagy factor and a target of the TOR kinase signaling pathway. The encoded protein is essential for autophagosome formation and mitophagy. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG13	NM_001346311.2	c.1576-935C>T		intron_variant		ENST00000683050.1	NP_001333240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG13	ENST00000683050.1	c.1576-935C>T		intron_variant			NM_001346311.2	ENSP00000507809	A1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72105 AN: 152034 Hom.: 20166 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.474 AC: 72093 AN: 152152 Hom.: 20158 Cov.: 33 AF XY: 0.473 AC XY: 35222 AN XY: 74388

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.514

Alfa AF: 0.587 Hom.: 36692

Bravo AF: 0.456

Asia WGS AF: 0.417 AC: 1457 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	7.9
DANN	Benign	0.63

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: rs4752926; hg19: chr11-46692870;