1-32895397-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000373463.8(TMEM54):c.502G>A(p.Val168Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,902 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V168L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000373463.8 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM54 | NM_033504.4 | c.502G>A | p.Val168Met | missense_variant | 5/6 | ENST00000373463.8 | NP_277039.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM54 | ENST00000373463.8 | c.502G>A | p.Val168Met | missense_variant | 5/6 | 1 | NM_033504.4 | ENSP00000362562.3 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250328Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135416
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461690Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727134
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.502G>A (p.V168M) alteration is located in exon 5 (coding exon 5) of the TMEM54 gene. This alteration results from a G to A substitution at nucleotide position 502, causing the valine (V) at amino acid position 168 to be replaced by a methionine (M). 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