rs4024308
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_004085.4(TIMM8A):c.*505_*506insGAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.37 ( 8763 hom., 11391 hem., cov: 11)
Exomes 𝑓: 0.18 ( 10090 hom. 33384 hem. )
Failed GnomAD Quality Control
Consequence
TIMM8A
NM_004085.4 3_prime_UTR
NM_004085.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.37
Genes affected
TIMM8A (HGNC:11817): (translocase of inner mitochondrial membrane 8A) This translocase is involved in the import and insertion of hydrophobic membrane proteins from the cytoplasm into the mitochondrial inner membrane. The gene is mutated in Mohr-Tranebjaerg syndrome/Deafness Dystonia Syndrome (MTS/DDS) and it is postulated that MTS/DDS is a mitochondrial disease caused by a defective mitochondrial protein import system. Defects in this gene also cause Jensen syndrome; an X-linked disease with opticoacoustic nerve atrophy and muscle weakness. This protein, along with TIMM13, forms a 70 kDa heterohexamer. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
?
Variant X-101345993-G-GATC is Benign according to our data. Variant chrX-101345993-G-GATC is described in ClinVar as [Benign]. Clinvar id is 21394.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TIMM8A | NM_004085.4 | c.*505_*506insGAT | 3_prime_UTR_variant | 2/2 | ENST00000372902.4 | ||
TIMM8A | NM_001145951.2 | c.*2393_*2394insGAT | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TIMM8A | ENST00000372902.4 | c.*505_*506insGAT | 3_prime_UTR_variant | 2/2 | 1 | NM_004085.4 | P1 | ||
TIMM8A | ENST00000644112.2 | c.*2393_*2394insGAT | 3_prime_UTR_variant | 2/2 | |||||
TIMM8A | ENST00000647480.1 | n.1316_1317insGAT | non_coding_transcript_exon_variant | 2/2 | |||||
TIMM8A | ENST00000645279.1 | c.*993_*994insGAT | 3_prime_UTR_variant, NMD_transcript_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.369 AC: 40476AN: 109769Hom.: 8757 Cov.: 11 AF XY: 0.353 AC XY: 11339AN XY: 32127
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.177 AC: 113854AN: 642029Hom.: 10090 Cov.: 19 AF XY: 0.174 AC XY: 33384AN XY: 191905
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.369 AC: 40540AN: 109823Hom.: 8763 Cov.: 11 AF XY: 0.354 AC XY: 11391AN XY: 32193
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Deafness dystonia syndrome Benign:1
Benign, no assertion criteria provided | curation | GeneReviews | Feb 06, 2003 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at