5-82011593-C-T

Variant summary

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

The NM_031482.5(ATG10):c.108+23915C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,116 control chromosomes in the GnomAD database, including 26,687 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 0.57 (26687 hom., cov: 32)
• Consequence: ATG10 NM_031482.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG10	NM_031482.5	c.108+23915C>T		intron_variant		ENST00000282185.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG10	ENST00000282185.8	c.108+23915C>T		intron_variant		1	NM_031482.5	P1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86836 AN: 151998 Hom.: 26658 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.571 AC: 86900 AN: 152116 Hom.: 26687 Cov.: 32 AF XY: 0.576 AC XY: 42847 AN XY: 74368

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.588

Alfa AF: 0.635 Hom.: 44017

Bravo AF: 0.565

Asia WGS AF: 0.782 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.0
Dann	Benign	0.44

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: rs10514231; hg19: chr5-81307412;