5-82255658-A-G

Variant names:

• chr5-82255658-A-G
• rs2115467
• NM_031482.5:c.*1595A>G

Variant summary

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

The NM_031482.5(ATG10):​c.*1595A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,060 control chromosomes in the GnomAD database, including 15,362 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 0.42 (15349 hom., cov: 31)
  • Exomes 𝑓: 0.61 (13 hom.)
• Consequence: ATG10 NM_031482.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATG10	NM_031482.5	c.*1595A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000282185.8	NP_113670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATG10	ENST00000282185.8	c.*1595A>G		3_prime_UTR_variant	Exon 8 of 8	1	NM_031482.5	ENSP00000282185.3
ATG10	ENST00000508814.5	n.260+2999A>G		intron_variant	Intron 3 of 3	3
ATG10	ENST00000514253.2	n.192-20487A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63382 AN: 151868 Hom.: 15331 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.424

GnomAD4 exome AF: 0.608 AC: 45 AN: 74 Hom.: 13 Cov.: 0 AF XY: 0.597 AC XY: 37 AN XY: 62

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 4 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.617 AC: 37 AN: 60

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.417 AC: 63413 AN: 151986 Hom.: 15349 Cov.: 31 AF XY: 0.427 AC XY: 31683 AN XY: 74278

African (AFR) AF: 0.196 AC: 8141 AN: 41454

American (AMR) AF: 0.550 AC: 8406 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1393 AN: 3468

East Asian (EAS) AF: 0.908 AC: 4677 AN: 5152

South Asian (SAS) AF: 0.604 AC: 2904 AN: 4804

European-Finnish (FIN) AF: 0.491 AC: 5176 AN: 10546

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31422 AN: 67970

Other (OTH) AF: 0.429 AC: 908 AN: 2116

Alfa AF: 0.422 Hom.: 2459

Bravo AF: 0.412

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.59
PhyloP100		-0.49
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: rs2115467; hg19: chr5-81551477;