12-10190099-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001384896.1(TMEM52B):c.511A>G(p.Thr171Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001384896.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM52B | NM_001384896.1 | c.511A>G | p.Thr171Ala | missense_variant | 5/5 | ENST00000543484.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM52B | ENST00000543484.2 | c.511A>G | p.Thr171Ala | missense_variant | 5/5 | 4 | NM_001384896.1 | P1 | |
TMEM52B | ENST00000298530.7 | c.451A>G | p.Thr151Ala | missense_variant | 4/4 | 1 | |||
TMEM52B | ENST00000381923.6 | c.511A>G | p.Thr171Ala | missense_variant | 6/6 | 5 | P1 | ||
TMEM52B | ENST00000546153.1 | n.397A>G | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251456Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135914
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461894Hom.: 0 Cov.: 31 AF XY: 0.0000413 AC XY: 30AN XY: 727248
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 24, 2022 | The c.451A>G (p.T151A) alteration is located in exon 4 (coding exon 4) of the TMEM52B gene. This alteration results from a A to G substitution at nucleotide position 451, causing the threonine (T) at amino acid position 151 to be replaced by an alanine (A). 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