rs56290633
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001128917.2(TOMM40):c.644-2204T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000011 ( 0 hom., cov: 13)
Failed GnomAD Quality Control
Consequence
TOMM40
NM_001128917.2 intron
NM_001128917.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.808
Genes affected
TOMM40 (HGNC:18001): (translocase of outer mitochondrial membrane 40) The protein encoded by this gene is localized in the outer membrane of the mitochondria. It is the channel-forming subunit of the translocase of the mitochondrial outer membrane (TOM) complex that is essential for import of protein precursors into mitochondria. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOMM40 | NM_001128917.2 | c.644-2204T>A | intron_variant | ENST00000426677.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOMM40 | ENST00000426677.7 | c.644-2204T>A | intron_variant | 1 | NM_001128917.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 88212Hom.: 0 Cov.: 13 FAILED QC
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000113 AC: 1AN: 88218Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0AN XY: 40152
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
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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