5-82257996-A-G

Variant names:

• chr5-82257996-A-G
• rs4703879
• ENST00000866604.1:c.*4+4567A>G

Variant summary

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

The ENST00000866604.1(ATG10):​c.*4+4567A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,138 control chromosomes in the GnomAD database, including 49,960 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 (49960 hom., cov: 32)
• Consequence: ATG10 ENST00000866604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 14 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000866604.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATG10	ENST00000866604.1		c.*4+4567A>G		intron	N/A	ENSP00000536663.1
	ATG10	ENST00000508814.5	TSL:3	n.260+5337A>G		intron	N/A
	ATG10	ENST00000514253.2	TSL:3	n.192-18149A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122747 AN: 152020 Hom.: 49901 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.808 AC: 122862 AN: 152138 Hom.: 49960 Cov.: 32 AF XY: 0.811 AC XY: 60280 AN XY: 74362

African (AFR) AF: 0.880 AC: 36537 AN: 41510

American (AMR) AF: 0.831 AC: 12694 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5110 AN: 5170

South Asian (SAS) AF: 0.838 AC: 4033 AN: 4812

European-Finnish (FIN) AF: 0.797 AC: 8429 AN: 10574

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51247 AN: 68008

Other (OTH) AF: 0.792 AC: 1675 AN: 2114

Alfa AF: 0.761 Hom.: 19128

Bravo AF: 0.814

Asia WGS AF: 0.889 AC: 3091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.35
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4703879; hg19: chr5-81553815;