rs12289253
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000313236.10(TMEM25):āc.1025A>Cā(p.Gln342Pro) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q342R) has been classified as Likely benign.
Frequency
Consequence
ENST00000313236.10 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM25 | NM_032780.4 | c.1025A>C | p.Gln342Pro | missense_variant, splice_region_variant | 8/9 | ENST00000313236.10 | NP_116169.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM25 | ENST00000313236.10 | c.1025A>C | p.Gln342Pro | missense_variant, splice_region_variant | 8/9 | 1 | NM_032780.4 | ENSP00000315635 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151988Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248506Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134702
GnomAD4 exome Cov.: 37
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at