18-68677090-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019022.5(TMX3):c.1208G>T(p.Gly403Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019022.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251008Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135638
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461594Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727092
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1208G>T (p.G403V) alteration is located in exon 16 (coding exon 16) of the TMX3 gene. This alteration results from a G to T substitution at nucleotide position 1208, causing the glycine (G) at amino acid position 403 to be replaced by a valine (V). 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