Variant rs148216086 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_005015.5(OXA1L):c.1265_1267dup(p.Ser422dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,611,336 control chromosomes in the GnomAD database, including 60,630 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 4869 hom., cov: 24)

Exomes 𝑓: 0.27 ( 55761 hom. )

Consequence

OXA1L
NM_005015.5 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.11

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 -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_005015.5. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 14-22771504-T-TAGC is Benign according to our data. Variant chr14-22771504-T-TAGC is described in ClinVar as [Benign]. Clinvar id is 403461.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OXA1L	NM_005015.5 linkuse as main transcript	c.1265_1267dup	p.Ser422dup	inframe_insertion	10/10	ENST00000612549.6	NP_005006.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OXA1L	ENST00000612549.6 linkuse as main transcript	c.1265_1267dup	p.Ser422dup	inframe_insertion	10/10	1	NM_005015.5	ENSP00000483491	P1

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37865

AN:

151794

Hom.:

4865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.395

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.364

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.274

GnomAD3 exomes

AF:

0.257

AC:

64521

AN:

251312

Hom.:

8792

AF XY:

0.266

AC XY:

36094

AN XY:

135812

show subpopulations

Gnomad AFR exome

AF:

0.204

Gnomad AMR exome

AF:

0.221

Gnomad ASJ exome

AF:

0.237

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.362

Gnomad FIN exome

AF:

0.226

Gnomad NFE exome

AF:

0.275

Gnomad OTH exome

AF:

0.273

GnomAD4 exome

AF:

0.274

AC:

400026

AN:

1459424

Hom.:

55761

Cov.:

AF XY:

0.278

AC XY:

201730

AN XY:

726078

show subpopulations

Gnomad4 AFR exome

AF:

0.205

Gnomad4 AMR exome

AF:

0.224

Gnomad4 ASJ exome

AF:

0.242

Gnomad4 EAS exome

AF:

0.152

Gnomad4 SAS exome

AF:

0.361

Gnomad4 FIN exome

AF:

0.229

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.268

GnomAD4 genome

AF:

0.249

AC:

37896

AN:

151912

Hom.:

4869

Cov.:

AF XY:

0.249

AC XY:

18478

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.206

Gnomad4 AMR

AF:

0.233

Gnomad4 ASJ

AF:

0.245

Gnomad4 EAS

AF:

0.147

Gnomad4 SAS

AF:

0.364

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.278

Alfa

AF:

0.192

Hom.:

604

Asia WGS

AF:

0.277

AC:

964

AN:

3478

EpiCase

AF:

0.290

EpiControl

AF:

0.285

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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