22-36476813-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012473.4(TXN2):āc.307A>Gā(p.Met103Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,613,980 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 (ā ).
Frequency
Consequence
NM_012473.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXN2 | NM_012473.4 | c.307A>G | p.Met103Val | missense_variant | 3/4 | ENST00000216185.7 | |
TXN2 | XM_006724226.2 | c.307A>G | p.Met103Val | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXN2 | ENST00000216185.7 | c.307A>G | p.Met103Val | missense_variant | 3/4 | 1 | NM_012473.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251490Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135920
GnomAD4 exome AF: 0.000143 AC: 209AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.000139 AC XY: 101AN XY: 727248
GnomAD4 genome AF: 0.000105 AC: 16AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74294
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 103 of the TXN2 protein (p.Met103Val). This variant is present in population databases (rs201787436, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with TXN2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1899123). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at