chr5-140644233-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018502.5(TMCO6):c.1200+39C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 1,594,126 control chromosomes in the GnomAD database, including 154,937 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 0.41 ( 13375 hom., cov: 32)
Exomes 𝑓: 0.44 ( 141562 hom. )
Consequence
TMCO6
NM_018502.5 intron
NM_018502.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.354
Genes affected
TMCO6 (HGNC:28814): (transmembrane and coiled-coil domains 6) Predicted to enable nuclear import signal receptor activity. Predicted to be involved in protein import into nucleus. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
NDUFA2 (HGNC:7685): (NADH:ubiquinone oxidoreductase subunit A2) The encoded protein is a subunit of the hydrophobic protein fraction of the NADH:ubiquinone oxidoreductase (complex 1), the first enzyme complex in the electron transport chain located in the inner mitochondrial membrane, and may be involved in regulating complex I activity or its assembly via assistance in redox processes. Mutations in this gene are associated with Leigh syndrome, an early-onset progressive neurodegenerative disorder. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
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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=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMCO6 | NM_018502.5 | c.1200+39C>T | intron_variant | ENST00000394671.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMCO6 | ENST00000394671.8 | c.1200+39C>T | intron_variant | 2 | NM_018502.5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.413 AC: 62813AN: 151930Hom.: 13365 Cov.: 32
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GnomAD3 exomes AF: 0.434 AC: 108057AN: 249160Hom.: 23826 AF XY: 0.436 AC XY: 58986AN XY: 135146
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GnomAD4 exome AF: 0.442 AC: 637168AN: 1442078Hom.: 141562 Cov.: 29 AF XY: 0.443 AC XY: 318601AN XY: 718594
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GnomAD4 genome AF: 0.413 AC: 62846AN: 152048Hom.: 13375 Cov.: 32 AF XY: 0.410 AC XY: 30498AN XY: 74350
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at