Variant 21-33909117-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001697.3(ATP5PO):c.293A>G(p.Lys98Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0895 in 1,612,302 control chromosomes in the GnomAD database, including 7,003 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 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 0.088 ( 638 hom., cov: 33)

Exomes 𝑓: 0.090 ( 6365 hom. )

Consequence

ATP5PO
NM_001697.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.85

Variant links:

Genes affected

ATP5PO (HGNC:850): (ATP synthase peripheral stalk subunit OSCP) The protein encoded by this gene is a component of the F-type ATPase found in the mitochondrial matrix. F-type ATPases are composed of a catalytic core and a membrane proton channel. The encoded protein appears to be part of the connector linking these two components and may be involved in transmission of conformational changes or proton conductance. [provided by RefSeq, Jul 2008]

ATP5PO links:

ENSG00000249209 (HGNC:):

ENSG00000249209 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=0.0022473037).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP5PO	NM_001697.3 linkuse as main transcript	c.293A>G	p.Lys98Arg	missense_variant	4/7	ENST00000290299.7	NP_001688.1	P48047

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP5PO	ENST00000290299.7 linkuse as main transcript	c.293A>G	p.Lys98Arg	missense_variant	4/7	1	NM_001697.3	ENSP00000290299.2		P48047
ENSG00000249209	ENST00000429238.2 linkuse as main transcript	c.293A>G	p.Lys98Arg	missense_variant	5/8	5		ENSP00000394107.2		H7C0C1

Frequencies

GnomAD3 genomes

AF:

0.0876

AC:

13337

AN:

152186

Hom.:

638

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.133

Gnomad AMR

AF:

0.0618

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.0165

Gnomad SAS

AF:

0.0809

Gnomad FIN

AF:

0.0523

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0937

Gnomad OTH

AF:

0.0947

GnomAD3 exomes

AF:

0.0794

AC:

19969

AN:

251386

Hom.:

968

AF XY:

0.0813

AC XY:

11043

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.0991

Gnomad AMR exome

AF:

0.0452

Gnomad ASJ exome

AF:

0.119

Gnomad EAS exome

AF:

0.0163

Gnomad SAS exome

AF:

0.0830

Gnomad FIN exome

AF:

0.0539

Gnomad NFE exome

AF:

0.0974

Gnomad OTH exome

AF:

0.0833

GnomAD4 exome

AF:

0.0896

AC:

130885

AN:

1459998

Hom.:

6365

Cov.:

AF XY:

0.0896

AC XY:

65074

AN XY:

726430

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0475

Gnomad4 ASJ exome

AF:

0.116

Gnomad4 EAS exome

AF:

0.0122

Gnomad4 SAS exome

AF:

0.0844

Gnomad4 FIN exome

AF:

0.0535

Gnomad4 NFE exome

AF:

0.0957

Gnomad4 OTH exome

AF:

0.0849

GnomAD4 genome

AF:

0.0877

AC:

13356

AN:

152304

Hom.:

638

Cov.:

AF XY:

0.0841

AC XY:

6261

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.0617

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.0164

Gnomad4 SAS

AF:

0.0816

Gnomad4 FIN

AF:

0.0523

Gnomad4 NFE

AF:

0.0938

Gnomad4 OTH

AF:

0.0938

Alfa

AF:

0.0938

Hom.:

1199

Bravo

AF:

0.0895

TwinsUK

AF:

0.0903

AC:

335

ALSPAC

AF:

0.0955

AC:

368

ESP6500AA

AF:

0.0971

AC:

428

ESP6500EA

AF:

0.0986

AC:

848

ExAC

AF:

0.0820

AC:

9953

Asia WGS

AF:

0.0510

AC:

176

AN:

3478

EpiCase

AF:

0.0938

EpiControl

AF:

0.0933

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.11

.;T

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.19

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.75

T;T

MetaRNN

Benign

0.0022

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

2.0

.;M

PROVEAN

Benign

-2.2

.;N

REVEL

Benign

0.11

Sift

Benign

0.082

.;T

Sift4G

Benign

0.10

.;T

Polyphen

0.010

.;B

Vest4

0.065

MPC

0.088

ClinPred

0.028

GERP RS

4.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.16

gMVP

0.50

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