Variant 14-22766599-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000285848.9(OXA1L):c.78G>A(p.Leu26Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 1,613,984 control chromosomes in the GnomAD database, including 162,383 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 12431 hom., cov: 33)

Exomes 𝑓: 0.45 ( 149952 hom. )

Consequence

OXA1L
ENST00000285848.9 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.785

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:

OXA1L-DT (HGNC:55448): (OXA1L divergent transcript)

OXA1L-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 14-22766599-G-A is Benign according to our data. Variant chr14-22766599-G-A is described in ClinVar as [Benign]. Clinvar id is 1241886.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.785 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
OXA1L-DT	XR_001750638.3 link	n.-37C>T	upstream_gene_variant
OXA1L-DT	XR_007064071.1 link	n.-37C>T	upstream_gene_variant
OXA1L-DT	XR_007064072.1 link	n.-37C>T	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	Protein	UniProt
OXA1L	ENST00000285848.9 link	c.78G>A	p.Leu26Leu	synonymous_variant	1/10	1	ENSP00000285848.5	J3KNA0
OXA1L-DT	ENST00000553792.1 link	n.-39C>T		upstream_gene_variant		5
OXA1L-DT	ENST00000554857.5 link	n.-37C>T		upstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55747

AN:

152050

Hom.:

12427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.469

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.371

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.400

GnomAD3 exomes

AF:

0.457

AC:

114931

AN:

251440

Hom.:

28857

AF XY:

0.451

AC XY:

61292

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.638

Gnomad ASJ exome

AF:

0.484

Gnomad EAS exome

AF:

0.715

Gnomad SAS exome

AF:

0.369

Gnomad FIN exome

AF:

0.365

Gnomad NFE exome

AF:

0.449

Gnomad OTH exome

AF:

0.454

GnomAD4 exome

AF:

0.446

AC:

651525

AN:

1461816

Hom.:

149952

Cov.:

AF XY:

0.443

AC XY:

322226

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.0993

Gnomad4 AMR exome

AF:

0.625

Gnomad4 ASJ exome

AF:

0.480

Gnomad4 EAS exome

AF:

0.648

Gnomad4 SAS exome

AF:

0.369

Gnomad4 FIN exome

AF:

0.362

Gnomad4 NFE exome

AF:

0.451

Gnomad4 OTH exome

AF:

0.443

GnomAD4 genome

AF:

0.366

AC:

55766

AN:

152168

Hom.:

12431

Cov.:

AF XY:

0.368

AC XY:

27369

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.549

Gnomad4 ASJ

AF:

0.469

Gnomad4 EAS

AF:

0.684

Gnomad4 SAS

AF:

0.366

Gnomad4 FIN

AF:

0.371

Gnomad4 NFE

AF:

0.450

Gnomad4 OTH

AF:

0.402

Alfa

AF:

0.436

Hom.:

19115

Bravo

AF:

0.373

Asia WGS

AF:

0.501

AC:

1742

AN:

3478

EpiCase

AF:

0.443

EpiControl

AF:

0.451

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	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.48

DANN

Benign

0.83

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