12-10179610-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153022.4(TMEM52B):c.20C>G(p.Pro7Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153022.4 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 |
---|---|---|---|---|---|---|---|---|
TMEM52B | NM_001384896.1 | c.36C>G | p.Ala12Ala | synonymous_variant | Exon 1 of 5 | ENST00000543484.2 | NP_001371825.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM52B | ENST00000298530.7 | c.20C>G | p.Pro7Arg | missense_variant | Exon 1 of 4 | 1 | ENSP00000298530.3 | |||
TMEM52B | ENST00000543484.2 | c.36C>G | p.Ala12Ala | synonymous_variant | Exon 1 of 5 | 4 | NM_001384896.1 | ENSP00000445582.2 | ||
TMEM52B | ENST00000381923.6 | c.36C>G | p.Ala12Ala | synonymous_variant | Exon 2 of 6 | 5 | ENSP00000371348.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461878Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.20C>G (p.P7R) alteration is located in exon 1 (coding exon 1) of the TMEM52B gene. This alteration results from a C to G substitution at nucleotide position 20, causing the proline (P) at amino acid position 7 to be replaced by an arginine (R). 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