1-1918349-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178545.4(TMEM52):c.253G>A(p.Ala85Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 1,460,596 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. A85E) has been classified as Uncertain significance.
Frequency
Consequence
NM_178545.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM52 | NM_178545.4 | c.253G>A | p.Ala85Thr | missense_variant | Exon 4 of 5 | ENST00000310991.8 | NP_848640.1 | |
TMEM52 | XM_047419236.1 | c.346G>A | p.Ala116Thr | missense_variant | Exon 3 of 4 | XP_047275192.1 | ||
TMEM52 | XM_047419237.1 | c.304G>A | p.Ala102Thr | missense_variant | Exon 2 of 3 | XP_047275193.1 | ||
TMEM52 | XM_047419240.1 | c.211G>A | p.Ala71Thr | missense_variant | Exon 3 of 4 | XP_047275196.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249224Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135414
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460596Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 726592
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.253G>A (p.A85T) alteration is located in exon 4 (coding exon 4) of the TMEM52 gene. This alteration results from a G to A substitution at nucleotide position 253, causing the alanine (A) at amino acid position 85 to be replaced by a threonine (T). 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