rs201254775
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001128917.2(TOMM40):c.607G>A(p.Val203Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000855 in 1,531,410 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001128917.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000127 AC: 24AN: 188644Hom.: 0 AF XY: 0.000120 AC XY: 12AN XY: 99792
GnomAD4 exome AF: 0.0000834 AC: 115AN: 1379226Hom.: 1 Cov.: 31 AF XY: 0.0000872 AC XY: 59AN XY: 676960
GnomAD4 genome AF: 0.000105 AC: 16AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.607G>A (p.V203I) alteration is located in exon 6 (coding exon 5) of the TOMM40 gene. This alteration results from a G to A substitution at nucleotide position 607, causing the valine (V) at amino acid position 203 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at