rs2286498
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019059.5(TOMM7):c.152+115A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 989,414 control chromosomes in the GnomAD database, including 93,122 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 0.48 ( 19431 hom., cov: 32)
Exomes 𝑓: 0.40 ( 73691 hom. )
Consequence
TOMM7
NM_019059.5 intron
NM_019059.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.53
Genes affected
TOMM7 (HGNC:21648): (translocase of outer mitochondrial membrane 7) This gene encodes a subunit of the translocase of the outer mitochondrial membrane. The encoded protein regulates the assembly and stability of the translocase complex. [provided by RefSeq, Oct 2012]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOMM7 | NM_019059.5 | c.152+115A>G | intron_variant | ENST00000358435.9 | |||
TOMM7 | NR_168014.1 | n.178+115A>G | intron_variant, non_coding_transcript_variant | ||||
TOMM7 | NR_168015.1 | n.130-4700A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOMM7 | ENST00000358435.9 | c.152+115A>G | intron_variant | 1 | NM_019059.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.481 AC: 73045AN: 151868Hom.: 19402 Cov.: 32
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GnomAD4 exome AF: 0.401 AC: 335908AN: 837424Hom.: 73691 Cov.: 11 AF XY: 0.403 AC XY: 174144AN XY: 432538
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GnomAD4 genome ? AF: 0.481 AC: 73135AN: 151990Hom.: 19431 Cov.: 32 AF XY: 0.484 AC XY: 36004AN XY: 74316
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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