rs17218354
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002493.5(NDUFB6):c.*703T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 342,892 control chromosomes in the GnomAD database, including 29,990 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 ( 12168 hom., cov: 31)
Exomes 𝑓: 0.41 ( 17822 hom. )
Consequence
NDUFB6
NM_002493.5 3_prime_UTR
NM_002493.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.716
Genes affected
NDUFB6 (HGNC:7701): (NADH:ubiquinone oxidoreductase subunit B6) The protein encoded by this gene is a subunit of the multisubunit NADH:ubiquinone oxidoreductase (complex I). Mammalian complex I is composed of 45 different subunits. It locates at the mitochondrial inner membrane. This protein has NADH dehydrogenase activity and oxidoreductase activity. It transfers electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Alternative splicing occurs at this locus and three transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jan 2011]
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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=-0.56).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFB6 | NM_002493.5 | c.*703T>C | 3_prime_UTR_variant | 4/4 | ENST00000379847.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDUFB6 | ENST00000379847.8 | c.*703T>C | 3_prime_UTR_variant | 4/4 | 1 | NM_002493.5 | P1 | ||
SMIM27 | ENST00000451672.2 | c.45+694A>G | intron_variant | ||||||
SMIM27 | ENST00000425533.1 | c.45+694A>G | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.390 AC: 59185AN: 151734Hom.: 12163 Cov.: 31
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GnomAD4 exome AF: 0.412 AC: 78667AN: 191042Hom.: 17822 Cov.: 0 AF XY: 0.416 AC XY: 41649AN XY: 100082
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GnomAD4 genome ? AF: 0.390 AC: 59199AN: 151850Hom.: 12168 Cov.: 31 AF XY: 0.386 AC XY: 28659AN XY: 74198
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at