NM_019022.5:c.925G>A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_019022.5(TMX3):c.925G>A(p.Val309Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00313 in 1,574,074 control chromosomes in the GnomAD database, including 15 homozygotes. 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 Likely benign (no stars).
Frequency
Consequence
NM_019022.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMX3 | ENST00000299608.7 | c.925G>A | p.Val309Ile | missense_variant | Exon 14 of 16 | 1 | NM_019022.5 | ENSP00000299608.2 | ||
TMX3 | ENST00000564631.5 | n.*609G>A | non_coding_transcript_exon_variant | Exon 13 of 15 | 1 | ENSP00000456587.1 | ||||
TMX3 | ENST00000564631.5 | n.*609G>A | 3_prime_UTR_variant | Exon 13 of 15 | 1 | ENSP00000456587.1 | ||||
TMX3 | ENST00000566135.1 | n.50G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00200 AC: 305AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00207 AC: 468AN: 225738Hom.: 2 AF XY: 0.00210 AC XY: 257AN XY: 122452
GnomAD4 exome AF: 0.00325 AC: 4616AN: 1421804Hom.: 15 Cov.: 29 AF XY: 0.00323 AC XY: 2276AN XY: 705310
GnomAD4 genome AF: 0.00201 AC: 306AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.00161 AC XY: 120AN XY: 74466
ClinVar
Submissions by phenotype
TMX3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at