Variant chr21-33909089-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000290299.7(ATP5PO):c.321T>C(p.Asn107Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 1,607,786 control chromosomes in the GnomAD database, including 384,644 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 36903 hom., cov: 32)

Exomes 𝑓: 0.69 ( 347741 hom. )

Consequence

ATP5PO
ENST00000290299.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.38

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 21-33909089-A-G is Benign according to our data. Variant chr21-33909089-A-G is described in ClinVar as [Benign]. Clinvar id is 1341585.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.713 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.321T>C	p.Asn107Asn	synonymous_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.321T>C	p.Asn107Asn	synonymous_variant	4/7	1	NM_001697.3	ENSP00000290299.2		P48047
ENSG00000249209	ENST00000429238.2 linkuse as main transcript	c.321T>C	p.Asn107Asn	synonymous_variant	5/8	5		ENSP00000394107.2		H7C0C1

Frequencies

GnomAD3 genomes

AF:

0.695

AC:

105636

AN:

151942

Hom.:

36859

Cov.:

show subpopulations

Gnomad AFR

AF:

0.720

Gnomad AMI

AF:

0.865

Gnomad AMR

AF:

0.634

Gnomad ASJ

AF:

0.728

Gnomad EAS

AF:

0.715

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.660

Gnomad MID

AF:

0.672

Gnomad NFE

AF:

0.692

Gnomad OTH

AF:

0.686

GnomAD3 exomes

AF:

0.684

AC:

171174

AN:

250156

Hom.:

59029

AF XY:

0.688

AC XY:

93132

AN XY:

135276

show subpopulations

Gnomad AFR exome

AF:

0.720

Gnomad AMR exome

AF:

0.596

Gnomad ASJ exome

AF:

0.725

Gnomad EAS exome

AF:

0.708

Gnomad SAS exome

AF:

0.731

Gnomad FIN exome

AF:

0.649

Gnomad NFE exome

AF:

0.692

Gnomad OTH exome

AF:

0.678

GnomAD4 exome

AF:

0.690

AC:

1004844

AN:

1455726

Hom.:

347741

Cov.:

AF XY:

0.692

AC XY:

501073

AN XY:

724522

show subpopulations

Gnomad4 AFR exome

AF:

0.718

Gnomad4 AMR exome

AF:

0.600

Gnomad4 ASJ exome

AF:

0.721

Gnomad4 EAS exome

AF:

0.695

Gnomad4 SAS exome

AF:

0.732

Gnomad4 FIN exome

AF:

0.651

Gnomad4 NFE exome

AF:

0.691

Gnomad4 OTH exome

AF:

0.688

GnomAD4 genome

AF:

0.695

AC:

105739

AN:

152060

Hom.:

36903

Cov.:

AF XY:

0.694

AC XY:

51579

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.720

Gnomad4 AMR

AF:

0.634

Gnomad4 ASJ

AF:

0.728

Gnomad4 EAS

AF:

0.715

Gnomad4 SAS

AF:

0.722

Gnomad4 FIN

AF:

0.660

Gnomad4 NFE

AF:

0.692

Gnomad4 OTH

AF:

0.690

Alfa

AF:

0.692

Hom.:

53312

Bravo

AF:

0.693

Asia WGS

AF:

0.749

AC:

2605

AN:

3478

EpiCase

AF:

0.693

EpiControl

AF:

0.694

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 11, 2022	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

4.5

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over