rs324913

Variant names:

• chr5-82093042-T-C
• rs324913
• NM_031482.5:c.216+34440T>C

Variant summary

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

The NM_031482.5(ATG10):​c.216+34440T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,064 control chromosomes in the GnomAD database, including 21,583 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 0.52 (21583 hom., cov: 32)
• Consequence: ATG10 NM_031482.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 7 publications found

Genes affected

ATG10 (HGNC:20315): (autophagy related 10) Autophagy is a process for the bulk degradation of cytosolic compartments by lysosomes. ATG10 is an E2-like enzyme involved in 2 ubiquitin-like modifications essential for autophagosome formation: ATG12 (MIM 609608)-ATG5 (MIM 604261) conjugation and modification of a soluble form of MAP-LC3 (MAP1LC3A; MIM 601242), a homolog of yeast Apg8, to a membrane-bound form (Nemoto et al., 2003 [PubMed 12890687]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG10	NM_031482.5	c.216+34440T>C		intron_variant	Intron 3 of 7	ENST00000282185.8	NP_113670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG10	ENST00000282185.8	c.216+34440T>C		intron_variant	Intron 3 of 7	1	NM_031482.5	ENSP00000282185.3

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79572 AN: 151946 Hom.: 21571 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.524 AC: 79607 AN: 152064 Hom.: 21583 Cov.: 32 AF XY: 0.524 AC XY: 38922 AN XY: 74340

African (AFR) AF: 0.633 AC: 26266 AN: 41480

American (AMR) AF: 0.405 AC: 6177 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1108 AN: 5178

South Asian (SAS) AF: 0.500 AC: 2411 AN: 4822

European-Finnish (FIN) AF: 0.556 AC: 5880 AN: 10578

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33890 AN: 67970

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.500 Hom.: 6245

Bravo AF: 0.514

Asia WGS AF: 0.354 AC: 1232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.1
DANN	Benign	0.40
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs324913; hg19: chr5-81388861;