chr12-94971904-A-AT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_018838.5(NDUFA12):c.258-285_258-284insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0195 in 557,988 control chromosomes in the GnomAD database, including 222 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.021 ( 96 hom., cov: 32)
Exomes 𝑓: 0.019 ( 126 hom. )
Consequence
NDUFA12
NM_018838.5 intron
NM_018838.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.314
Genes affected
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 12-94971904-A-AT is Benign according to our data. Variant chr12-94971904-A-AT is described in ClinVar as [Benign]. Clinvar id is 1291707.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0206 (3125/151358) while in subpopulation NFE AF= 0.0223 (1509/67812). AF 95% confidence interval is 0.0213. There are 96 homozygotes in gnomad4. There are 1788 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 96 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFA12 | NM_018838.5 | c.258-285_258-284insA | intron_variant | ENST00000327772.7 | |||
NDUFA12 | NM_001258338.2 | c.170-285_170-284insA | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFA12 | ENST00000327772.7 | c.258-285_258-284insA | intron_variant | 1 | NM_018838.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0207 AC: 3126AN: 151244Hom.: 96 Cov.: 32
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GnomAD4 exome AF: 0.0190 AC: 7737AN: 406630Hom.: 126 AF XY: 0.0179 AC XY: 3919AN XY: 218710
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 13, 2019 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at