Variant 12-94928357-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.394 in 453,596 control chromosomes in the GnomAD database, including 35,473 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 11743 hom., cov: 32)

Exomes 𝑓: 0.40 ( 23730 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Variant links:

Genes affected

(HGNC:):

links:

NDUFA12 (HGNC:23987): (NADH:ubiquinone oxidoreductase subunit A12) This gene encodes a protein which is part of mitochondrial complex 1, part of the oxidative phosphorylation system in mitochondria. Complex 1 transfers electrons to ubiquinone from NADH which establishes a proton gradient for the generation of ATP. Mutations in this gene are associated with Leigh syndrome due to mitochondrial complex 1 deficiency. Pseudogenes of this gene are located on chromosomes 5 and 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]

NDUFA12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.94928357C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFA12	ENST00000552205.6 linkuse as main transcript	n.258-94G>A		intron_variant		5		ENSP00000449144.2		H0YID5

Frequencies

GnomAD3 genomes

AF:

0.392

AC:

59526

AN:

151822

Hom.:

11735

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.334

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.393

GnomAD4 exome

AF:

0.395

AC:

119267

AN:

301656

Hom.:

23730

AF XY:

0.396

AC XY:

68097

AN XY:

171826

show subpopulations

Gnomad4 AFR exome

AF:

0.406

Gnomad4 AMR exome

AF:

0.424

Gnomad4 ASJ exome

AF:

0.376

Gnomad4 EAS exome

AF:

0.392

Gnomad4 SAS exome

AF:

0.410

Gnomad4 FIN exome

AF:

0.418

Gnomad4 NFE exome

AF:

0.385

Gnomad4 OTH exome

AF:

0.382

GnomAD4 genome

AF:

0.392

AC:

59558

AN:

151940

Hom.:

11743

Cov.:

AF XY:

0.395

AC XY:

29295

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.398

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.387

Gnomad4 EAS

AF:

0.381

Gnomad4 SAS

AF:

0.408

Gnomad4 FIN

AF:

0.428

Gnomad4 NFE

AF:

0.381

Gnomad4 OTH

AF:

0.389

Alfa

AF:

0.385

Hom.:

15311

Bravo

AF:

0.388

Asia WGS

AF:

0.406

AC:

1412

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.5

DANN

Benign

0.82

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over