chr11-67606525-C-CT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The ENST00000533876.1(ENSG00000255119):n.439dup variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 228,450 control chromosomes in the GnomAD database, including 26 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 12 hom., cov: 31)
Exomes 𝑓: 0.012 ( 14 hom. )
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.285
Genes affected
NDUFV1-DT (HGNC:26915): (NDUFV1 divergent transcript)
NDUFV1 (HGNC:7716): (NADH:ubiquinone oxidoreductase core subunit V1) The mitochondrial respiratory chain provides energy to cells via oxidative phosphorylation and consists of four membrane-bound electron-transporting protein complexes (I-IV) and an ATP synthase (complex V). This gene encodes a 51 kDa subunit of the NADH:ubiquinone oxidoreductase complex I; a large complex with at least 45 nuclear and mitochondrial encoded subunits that liberates electrons from NADH and channels them to ubiquinone. This subunit carries the NADH-binding site as well as flavin mononucleotide (FMN)- and Fe-S-biding sites. Defects in complex I are a common cause of mitochondrial dysfunction; a syndrome that occurs in approximately 1 in 10,000 live births. Mitochondrial complex I deficiency is linked to myopathies, encephalomyopathies, and neurodegenerative disorders such as Parkinson's disease and Leigh syndrome. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 11-67606525-C-CT is Benign according to our data. Variant chr11-67606525-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 1195099.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0113 (1717/152202) while in subpopulation NFE AF= 0.0174 (1184/67998). AF 95% confidence interval is 0.0166. There are 12 homozygotes in gnomad4. There are 790 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFV1-DT | NR_130935.1 | n.88+93_88+94insA | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000533876.1 | n.439dup | non_coding_transcript_exon_variant | 2/2 | 4 | |||||
NDUFV1-DT | ENST00000333139.3 | n.88+93_88+94insA | intron_variant, non_coding_transcript_variant | 2 | |||||
NDUFV1 | ENST00000647561.1 | c.-479dup | 5_prime_UTR_variant | 2/11 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0113 AC: 1718AN: 152084Hom.: 12 Cov.: 31
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GnomAD4 exome AF: 0.0120 AC: 912AN: 76248Hom.: 14 Cov.: 0 AF XY: 0.0114 AC XY: 463AN XY: 40678
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2019 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at