Variant 14-22766613-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000285848.9(OXA1L):c.92G>C(p.Trp31Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00287 in 1,614,176 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0029 ( 7 hom. )

Consequence

OXA1L
ENST00000285848.9 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.90

Variant links:

Genes affected

OXA1L (HGNC:8526): (OXA1L mitochondrial inner membrane protein) This gene encodes an evolutionarily conserved protein that is localized to the inner mitochondrial membrane. The encoded protein is essential for the translocation of the N-terminal tail of subunit 2 of cytochrome c oxidase, and is involved in the assembly of the cytochrome c oxidase and ATPase complexes of the mitochondrial respiratory chain. [provided by RefSeq, Jul 2016]

OXA1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0048783123).

BP6

Variant 14-22766613-G-C is Benign according to our data. Variant chr14-22766613-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2644074.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXA1L	ENST00000285848.9 linkuse as main transcript	c.92G>C	p.Trp31Ser	missense_variant	1/10	1		ENSP00000285848

Frequencies

GnomAD3 genomes

AF:

0.00252

AC:

384

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000627

Gnomad AMI

AF:

0.0669

Gnomad AMR

AF:

0.00137

Gnomad ASJ

AF:

0.00547

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00248

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00317

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00254

AC:

639

AN:

251482

Hom.:

AF XY:

0.00266

AC XY:

361

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.000615

Gnomad AMR exome

AF:

0.000549

Gnomad ASJ exome

AF:

0.00397

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00235

Gnomad FIN exome

AF:

0.00263

Gnomad NFE exome

AF:

0.00377

Gnomad OTH exome

AF:

0.00195

GnomAD4 exome

AF:

0.00290

AC:

4244

AN:

1461886

Hom.:

Cov.:

AF XY:

0.00288

AC XY:

2091

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.000538

Gnomad4 AMR exome

AF:

0.000626

Gnomad4 ASJ exome

AF:

0.00333

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00234

Gnomad4 FIN exome

AF:

0.00271

Gnomad4 NFE exome

AF:

0.00326

Gnomad4 OTH exome

AF:

0.00219

GnomAD4 genome

AF:

0.00251

AC:

383

AN:

152290

Hom.:

Cov.:

AF XY:

0.00222

AC XY:

165

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000626

Gnomad4 AMR

AF:

0.00137

Gnomad4 ASJ

AF:

0.00547

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.00318

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00294

Hom.:

Bravo

AF:

0.00269

TwinsUK

AF:

0.00243

AC:

ALSPAC

AF:

0.00467

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00326

AC:

ExAC

AF:

0.00278

AC:

338

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00267

EpiControl

AF:

0.00344

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

OXA1L: BP4, BS3:Supporting, BS1 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.42

CADD

Benign

9.7

DANN

Benign

0.76

Eigen

Benign

-0.31

Eigen_PC

Benign

-0.32

FATHMM_MKL

Benign

0.081

LIST_S2

Benign

0.21

T;.

M_CAP

Benign

0.0056

MetaRNN

Benign

0.0049

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.57

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.29

N;.

REVEL

Benign

0.11

Sift

Benign

0.20

T;.

Sift4G

Pathogenic

0.0

D;D

Vest4

0.23

MVP

0.65

MPC

0.10

ClinPred

0.064

GERP RS

5.2

gMVP

0.19

Splicing

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