Variant rs1864182 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.659C>A(p.Pro220His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,558,954 control chromosomes in the GnomAD database, including 246,004 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 0.48 ( 19865 hom., cov: 33)

Exomes 𝑓: 0.56 ( 226139 hom. )

Consequence

ATG10
NM_031482.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.142

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=9.702688E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATG10	NM_031482.5 linkuse as main transcript	c.659C>A	p.Pro220His	missense_variant	7/8	ENST00000282185.8	NP_113670.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATG10	ENST00000282185.8 linkuse as main transcript	c.659C>A	p.Pro220His	missense_variant	7/8	1	NM_031482.5	ENSP00000282185	P1	Q9H0Y0-1

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72535

AN:

152042

Hom.:

19844

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.373

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.470

Gnomad EAS

AF:

0.912

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.585

Gnomad MID

AF:

0.433

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.478

GnomAD3 exomes

AF:

0.588

AC:

147628

AN:

250936

Hom.:

46420

AF XY:

0.591

AC XY:

80095

AN XY:

135606

show subpopulations

Gnomad AFR exome

AF:

0.203

Gnomad AMR exome

AF:

0.708

Gnomad ASJ exome

AF:

0.463

Gnomad EAS exome

AF:

0.908

Gnomad SAS exome

AF:

0.667

Gnomad FIN exome

AF:

0.588

Gnomad NFE exome

AF:

0.547

Gnomad OTH exome

AF:

0.553

GnomAD4 exome

AF:

0.557

AC:

783417

AN:

1406794

Hom.:

226139

Cov.:

AF XY:

0.561

AC XY:

394604

AN XY:

702850

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.695

Gnomad4 ASJ exome

AF:

0.464

Gnomad4 EAS exome

AF:

0.941

Gnomad4 SAS exome

AF:

0.663

Gnomad4 FIN exome

AF:

0.590

Gnomad4 NFE exome

AF:

0.541

Gnomad4 OTH exome

AF:

0.540

GnomAD4 genome

AF:

0.477

AC:

72567

AN:

152160

Hom.:

19865

Cov.:

AF XY:

0.486

AC XY:

36125

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.213

Gnomad4 AMR

AF:

0.592

Gnomad4 ASJ

AF:

0.470

Gnomad4 EAS

AF:

0.912

Gnomad4 SAS

AF:

0.682

Gnomad4 FIN

AF:

0.585

Gnomad4 NFE

AF:

0.550

Gnomad4 OTH

AF:

0.485

Alfa

AF:

0.540

Hom.:

56385

Bravo

AF:

0.464

TwinsUK

AF:

0.562

AC:

2084

ALSPAC

AF:

0.536

AC:

2065

ESP6500AA

AF:

0.224

AC:

986

ESP6500EA

AF:

0.559

AC:

4809

ExAC

AF:

0.579

AC:

70259

Asia WGS

AF:

0.760

AC:

2643

AN:

3478

EpiCase

AF:

0.542

EpiControl

AF:

0.539

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

5.2

DANN

Benign

0.47

DEOGEN2

Benign

0.014

T;T

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.00032

LIST_S2

Benign

0.16

.;T

MetaRNN

Benign

9.7e-7

T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.0

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.32

PROVEAN

Benign

0.45

N;N

REVEL

Benign

0.049

Sift

Pathogenic

0.0

D;D

Polyphen

0.0

B;B

Vest4

0.024

MPC

0.52

ClinPred

0.0090

GERP RS

-2.7

Varity_R

0.088

gMVP

0.43

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

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