18-68677084-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019022.5(TMX3):c.1214A>G(p.Tyr405Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMX3 | NM_019022.5 | c.1214A>G | p.Tyr405Cys | missense_variant | 16/16 | ENST00000299608.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMX3 | ENST00000299608.7 | c.1214A>G | p.Tyr405Cys | missense_variant | 16/16 | 1 | NM_019022.5 | P1 | |
TMX3 | ENST00000564631.5 | c.*898A>G | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 1 | ||||
TMX3 | ENST00000566135.1 | n.339A>G | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
TMX3 | ENST00000578816.1 | n.225A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461600Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727098
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.1214A>G (p.Y405C) alteration is located in exon 16 (coding exon 16) of the TMX3 gene. This alteration results from a A to G substitution at nucleotide position 1214, causing the tyrosine (Y) at amino acid position 405 to be replaced by a cysteine (C). 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
Publications
No publications associated with this variant yet.