Variant rs1864183 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0820

Variant links:

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]

ATG10 links:

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ACMG classification

Classification made for transcript

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 linkuse as main transcript	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 linkuse as main transcript	c.635C>T	p.Thr212Met	missense_variant	7/8	1	NM_031482.5	P1	Q9H0Y0-1

Frequencies

GnomAD3 genomes

AF:

0.415

AC:

63036

AN:

151956

Hom.:

15130

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.478

AC XY:

345136

AN XY:

721396

show subpopulations

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.:

AF XY:

0.423

AC XY:

31459

AN XY:

74320

show subpopulations

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

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.90

DEOGEN2

Benign

0.014

T;T

Eigen

Benign

-0.99

Eigen_PC

Benign

-0.93

FATHMM_MKL

Benign

0.022

LIST_S2

Benign

0.59

.;T

MetaRNN

Benign

8.6e-7

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.28

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

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over