rs10119
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001128917.2(TOMM40):c.*247G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 411,388 control chromosomes in the GnomAD database, including 16,271 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 0.28 ( 6132 hom., cov: 33)
Exomes 𝑓: 0.27 ( 10139 hom. )
Consequence
TOMM40
NM_001128917.2 3_prime_UTR
NM_001128917.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.111
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOMM40 | NM_001128917.2 | c.*247G>A | 3_prime_UTR_variant | 9/9 | ENST00000426677.7 | ||
TOMM40 | NM_001128916.2 | c.*247G>A | 3_prime_UTR_variant | 10/10 | |||
TOMM40 | NM_006114.3 | c.*247G>A | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOMM40 | ENST00000426677.7 | c.*247G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_001128917.2 | P1 | ||
TOMM40 | ENST00000252487.9 | c.*247G>A | 3_prime_UTR_variant | 10/10 | 1 | P1 | |||
TOMM40 | ENST00000405636.6 | c.*247G>A | 3_prime_UTR_variant | 10/10 | 1 | P1 | |||
TOMM40 | ENST00000592434.5 | c.*2062G>A | 3_prime_UTR_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.279 AC: 42369AN: 152058Hom.: 6105 Cov.: 33
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GnomAD4 exome AF: 0.273 AC: 70647AN: 259212Hom.: 10139 Cov.: 4 AF XY: 0.271 AC XY: 36891AN XY: 136076
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GnomAD4 genome ? AF: 0.279 AC: 42455AN: 152176Hom.: 6132 Cov.: 33 AF XY: 0.277 AC XY: 20581AN XY: 74380
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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