5-82257996-A-G

Position:

• chr5-82257996-A-G

Variant summary

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

The ENST00000508814.5(ATG10):​n.260+5337A>G variant causes a intron, non coding transcript 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 ENST00000508814.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG10	ENST00000508814.5	n.260+5337A>G		intron_variant, non_coding_transcript_variant		3
ATG10	ENST00000514253.2	n.192-18149A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.792

Alfa AF: 0.757 Hom.: 10295

Bravo AF: 0.814

Asia WGS AF: 0.889 AC: 3091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4703879; hg19: chr5-81553815;