5-82011593-C-T

Variant names:

• chr5-82011593-C-T
• rs10514231
• NM_031482.5:c.108+23915C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 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=-0.86).
• 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 rank	MANE	Protein	UniProt
ATG10	NM_031482.5	c.108+23915C>T		intron_variant	Intron 2 of 7	ENST00000282185.8	NP_113670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG10	ENST00000282185.8	c.108+23915C>T		intron_variant	Intron 2 of 7	1	NM_031482.5	ENSP00000282185.3

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

African (AFR) AF: 0.344 AC: 14281 AN: 41470

American (AMR) AF: 0.679 AC: 10385 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1914 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4683 AN: 5184

South Asian (SAS) AF: 0.722 AC: 3482 AN: 4824

European-Finnish (FIN) AF: 0.614 AC: 6479 AN: 10560

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43934 AN: 68000

Other (OTH) AF: 0.588 AC: 1243 AN: 2114

Alfa AF: 0.622 Hom.: 99759

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
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10514231; hg19: chr5-81307412;