19-44892457-T-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001128917.2(TOMM40):āc.339T>Cā(p.Phe113Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,611,534 control chromosomes in the GnomAD database, including 46,154 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: š 0.29 ( 7174 hom., cov: 31)
Exomes š: 0.23 ( 38980 hom. )
Consequence
TOMM40
NM_001128917.2 synonymous
NM_001128917.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.40
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP7
Synonymous conserved (PhyloP=2.4 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.287 AC: 43614AN: 151764Hom.: 7146 Cov.: 31
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GnomAD3 exomes AF: 0.246 AC: 61815AN: 251406Hom.: 8162 AF XY: 0.237 AC XY: 32168AN XY: 135876
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GnomAD4 exome AF: 0.227 AC: 331325AN: 1459652Hom.: 38980 Cov.: 33 AF XY: 0.225 AC XY: 163564AN XY: 726170
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GnomAD4 genome AF: 0.288 AC: 43704AN: 151882Hom.: 7174 Cov.: 31 AF XY: 0.289 AC XY: 21480AN XY: 74228
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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