rs1485587

chr5-82031223-A-G

Variant summary

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

The NM_031482.5(ATG10):c.109-27272A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,952 control chromosomes in the GnomAD database, including 20,594 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 0.51 (20594 hom., cov: 32)
• Consequence: ATG10 NM_031482.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG10	NM_031482.5	c.109-27272A>G		intron_variant		ENST00000282185.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG10	ENST00000282185.8	c.109-27272A>G		intron_variant		1	NM_031482.5	P1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77777 AN: 151832 Hom.: 20588 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.512 AC: 77803 AN: 151952 Hom.: 20594 Cov.: 32 AF XY: 0.511 AC XY: 37949 AN XY: 74260

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.497

Alfa AF: 0.493 Hom.: 38553

Bravo AF: 0.505

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.57

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: rs1485587; hg19: chr5-81327042;