11-46673864-T-C

Variant names:

• chr11-46673864-T-C
• rs13448
• NM_001346311.2:c.*1532T>C

Variant summary

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

The NM_001346311.2(ATG13):​c.*1532T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,050 control chromosomes in the GnomAD database, including 8,567 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 0.33 (8560 hom., cov: 32)
  • Exomes 𝑓: 0.39 (7 hom.)
• Consequence: ATG13 NM_001346311.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 21 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG13	NM_001346311.2	c.*1532T>C		3_prime_UTR_variant	Exon 19 of 19	ENST00000683050.1	NP_001333240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG13	ENST00000683050.1	c.*1532T>C		3_prime_UTR_variant	Exon 19 of 19		NM_001346311.2	ENSP00000507809.1

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49516 AN: 151876 Hom.: 8540 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.393 AC: 22 AN: 56 Hom.: 7 Cov.: 0 AF XY: 0.425 AC XY: 17 AN XY: 40

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.333 AC: 16 AN: 48

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.326 AC: 49576 AN: 151994 Hom.: 8560 Cov.: 32 AF XY: 0.332 AC XY: 24651 AN XY: 74310

African (AFR) AF: 0.386 AC: 16011 AN: 41466

American (AMR) AF: 0.296 AC: 4520 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3339 AN: 5142

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4816

European-Finnish (FIN) AF: 0.363 AC: 3840 AN: 10574

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18395 AN: 67936

Other (OTH) AF: 0.286 AC: 606 AN: 2116

Alfa AF: 0.285 Hom.: 15505

Bravo AF: 0.327

Asia WGS AF: 0.415 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.83
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13448; hg19: chr11-46695414;