Variant 18-46084885-GT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000398752.11(ATP5F1A):c.1430-232del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 425,222 control chromosomes in the GnomAD database, including 4,374 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.099 ( 1041 hom., cov: 31)

Exomes 𝑓: 0.11 ( 3333 hom. )

Consequence

ATP5F1A
ENST00000398752.11 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0120

Variant links:

Genes affected

ATP5F1A (HGNC:823): (ATP synthase F1 subunit alpha) This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, using an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel consists of three main subunits (a, b, c). This gene encodes the alpha subunit of the catalytic core. Alternatively spliced transcript variants encoding the different isoforms have been identified. Pseudogenes of this gene are located on chromosomes 9, 2, and 16. [provided by RefSeq, Mar 2012]

ATP5F1A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 18-46084885-GT-G is Benign according to our data. Variant chr18-46084885-GT-G is described in ClinVar as [Benign]. Clinvar id is 1236688.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP5F1A	NM_004046.6 linkuse as main transcript	c.1430-232del		intron_variant		ENST00000398752.11	NP_004037.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP5F1A	ENST00000398752.11 linkuse as main transcript	c.1430-232del		intron_variant		1	NM_004046.6	ENSP00000381736	P1	P25705-1

Frequencies

GnomAD3 genomes

AF:

0.0990

AC:

15051

AN:

152016

Hom.:

1042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0809

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.0541

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0799

Gnomad OTH

AF:

0.0922

GnomAD4 exome

AF:

0.115

AC:

31399

AN:

273088

Hom.:

3333

Cov.:

AF XY:

0.113

AC XY:

15763

AN XY:

139820

show subpopulations

Gnomad4 AFR exome

AF:

0.0875

Gnomad4 AMR exome

AF:

0.168

Gnomad4 ASJ exome

AF:

0.0944

Gnomad4 EAS exome

AF:

0.454

Gnomad4 SAS exome

AF:

0.0409

Gnomad4 FIN exome

AF:

0.102

Gnomad4 NFE exome

AF:

0.0802

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.0990

AC:

15061

AN:

152134

Hom.:

1041

Cov.:

AF XY:

0.102

AC XY:

7559

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.0807

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.102

Gnomad4 EAS

AF:

0.392

Gnomad4 SAS

AF:

0.0545

Gnomad4 FIN

AF:

0.110

Gnomad4 NFE

AF:

0.0800

Gnomad4 OTH

AF:

0.0912

Alfa

AF:

0.0281

Hom.:

Bravo

AF:

0.106

Asia WGS

AF:

0.206

AC:

715

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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