rs6538566

chr12-94902782-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001749264.2(LOC105369915):n.404-5472T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 150,250 control chromosomes in the GnomAD database, including 44,488 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 0.77 (44488 hom., cov: 27)
• Consequence: LOC105369915 XR_001749264.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

Genes affected

LOC105369915 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369915	XR_001749264.2	n.404-5472T>G		intron_variant, non_coding_transcript_variant
LOC105369915	XR_945226.2	n.515-5472T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFA12	ENST00000552205.6	c.*180-5472T>G		intron_variant, NMD_transcript_variant		5
NDUFA12	ENST00000547447.1	n.273-5472T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.769 AC: 115428 AN: 150134 Hom.: 44454 Cov.: 27

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.775

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.769 AC: 115512 AN: 150250 Hom.: 44488 Cov.: 27 AF XY: 0.769 AC XY: 56243 AN XY: 73098

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.776

Alfa AF: 0.780 Hom.: 93093

Bravo AF: 0.774

Asia WGS AF: 0.749 AC: 2604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.5
Dann	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6538566; hg19: chr12-95296558;