Variant 11-85648050-A-AGACC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_032273.4(TMEM126A):c.-46_-45insACCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,122 control chromosomes in the GnomAD database, including 6,516 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6513 hom., cov: 22)

Exomes 𝑓: 0.16 ( 3 hom. )

Consequence

TMEM126A
NM_032273.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.564

Variant links:

Genes affected

TMEM126A (HGNC:25382): (transmembrane protein 126A) The protein encoded by this gene is a mitochondrial membrane protein of unknown function. Defects in this gene are a cause of optic atrophy type 7 (OPA7). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

TMEM126A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 11-85648050-A-AGACC is Benign according to our data. Variant chr11-85648050-A-AGACC is described in ClinVar as [Benign]. Clinvar id is 215269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM126A	NM_032273.4 link	c.-46_-45insACCG		5_prime_UTR_variant	1/5	ENST00000304511.7	NP_115649.1	Q9H061-1
TMEM126A	NM_001244735.2 link	c.-163_-162insACCG		5_prime_UTR_variant	1/4		NP_001231664.1	Q9H061-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM126A	ENST00000304511 link	c.-46_-45insACCG		5_prime_UTR_variant	1/5	1	NM_032273.4	ENSP00000306887.2		Q9H061-1

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42545

AN:

151804

Hom.:

6476

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.379

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.266

GnomAD4 exome

AF:

0.160

AC:

AN:

200

Hom.:

Cov.:

AF XY:

0.156

AC XY:

AN XY:

160

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.200

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.281

AC:

42638

AN:

151922

Hom.:

6513

Cov.:

AF XY:

0.289

AC XY:

21446

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.389

Gnomad4 AMR

AF:

0.323

Gnomad4 ASJ

AF:

0.234

Gnomad4 EAS

AF:

0.385

Gnomad4 SAS

AF:

0.378

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.245

Hom.:

606

Bravo

AF:

0.291

Asia WGS

AF:

0.404

AC:

1405

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, flagged submission

clinical testing

GeneDx

Apr 22, 2014

The variant is found in MITONUC-MITOP panel(s). -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 10, 2018

- -

Optic Atrophy, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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