rs891159

chr5-82195268-G-Achr5-82195268-G-Cchr5-82195268-G-T

Variant summary

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

The NM_031482.5(ATG10):c.453+16681G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,146 control chromosomes in the GnomAD database, including 49,797 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 0.81 (49797 hom., cov: 32)
• Consequence: ATG10 NM_031482.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG10	NM_031482.5	c.453+16681G>A		intron_variant		ENST00000282185.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG10	ENST00000282185.8	c.453+16681G>A		intron_variant		1	NM_031482.5	P1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122550 AN: 152028 Hom.: 49741 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.806 AC: 122661 AN: 152146 Hom.: 49797 Cov.: 32 AF XY: 0.809 AC XY: 60164 AN XY: 74362

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.792

Alfa AF: 0.758 Hom.: 23527

Bravo AF: 0.812

Asia WGS AF: 0.888 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.1
Dann	Benign	0.49

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: rs891159; hg19: chr5-81491087;