rs1864183

chr5-82253397-C-T

Variant summary

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

The NM_031482.5(ATG10):c.635C>T(p.Thr212Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 1,600,552 control chromosomes in the GnomAD database, including 186,484 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.41 (15150 hom., cov: 32)
  • Exomes 𝑓: 0.47 (171334 hom.)
• Consequence: ATG10 NM_031482.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

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 (MetaRNN=8.61997E-7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATG10	NM_031482.5	c.635C>T	p.Thr212Met	missense_variant	7/8	ENST00000282185.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG10	ENST00000282185.8	c.635C>T	p.Thr212Met	missense_variant	7/8	1	NM_031482.5	P1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63036 AN: 151956 Hom.: 15130 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.422

GnomAD3 exomes AF: 0.519 AC: 130333 AN: 251262 Hom.: 37054 AF XY: 0.518 AC XY: 70395 AN XY: 135808

Gnomad AFR exome AF: 0.189

Gnomad AMR exome AF: 0.680

Gnomad ASJ exome AF: 0.390

Gnomad EAS exome AF: 0.884

Gnomad SAS exome AF: 0.587

Gnomad FIN exome AF: 0.482

Gnomad NFE exome AF: 0.459

Gnomad OTH exome AF: 0.485

GnomAD4 exome AF: 0.474 AC: 686491 AN: 1448478 Hom.: 171334 Cov.: 32 AF XY: 0.478 AC XY: 345136 AN XY: 721396

Gnomad4 AFR exome AF: 0.186

Gnomad4 AMR exome AF: 0.664

Gnomad4 ASJ exome AF: 0.396

Gnomad4 EAS exome AF: 0.916

Gnomad4 SAS exome AF: 0.583

Gnomad4 FIN exome AF: 0.486

Gnomad4 NFE exome AF: 0.452

Gnomad4 OTH exome AF: 0.464

GnomAD4 genome AF: 0.415 AC: 63068 AN: 152074 Hom.: 15150 Cov.: 32 AF XY: 0.423 AC XY: 31459 AN XY: 74320

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.428

Alfa AF: 0.452 Hom.: 27689

Bravo AF: 0.410

TwinsUK AF: 0.461 AC: 1709

ALSPAC AF: 0.445 AC: 1716

ESP6500AA AF: 0.207 AC: 913

ESP6500EA AF: 0.465 AC: 3996

ExAC AF: 0.509 AC: 61821

Asia WGS AF: 0.715 AC: 2487 AN: 3478

EpiCase AF: 0.459

EpiControl AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.083
BayesDel_addAF	Benign	-0.76	T
BayesDel_noAF	Benign	-0.72
Cadd	Benign	13
Dann	Benign	0.90
DEOGEN2	Benign	0.014	T;T
Eigen	Benign	-0.99
Eigen_PC	Benign	-0.93
FATHMM_MKL	Benign	0.022	N
MetaRNN	Benign	8.6e-7	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N;N
MutationTaster	Benign	1.0	P;P
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-0.15	N;N
REVEL	Benign	0.072
Sift	Benign	0.14	T;T
Sift4G	Benign	0.15	T;T
Polyphen		0.11	B;B
Vest4		0.041
MPC		0.12
ClinPred		0.0069	T
GERP RS		1.6
Varity_R		0.027
gMVP		0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		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: rs1864183; hg19: chr5-81549216; COSMIC: COSV56424284; COSMIC: COSV56424284;