rs6589664
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_032780.4(TMEM25):c.897G>A(p.Pro299=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,613,730 control chromosomes in the GnomAD database, including 69,962 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.27 ( 6150 hom., cov: 31)
Exomes 𝑓: 0.29 ( 63812 hom. )
Consequence
TMEM25
NM_032780.4 synonymous
NM_032780.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.70
Genes affected
TMEM25 (HGNC:25890): (transmembrane protein 25) Predicted to be involved in negative regulation of excitatory postsynaptic potential and regulation of protein stability. Predicted to be located in late endosome and lysosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP7
?
Synonymous conserved (PhyloP=-2.7 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM25 | NM_032780.4 | c.897G>A | p.Pro299= | synonymous_variant | 7/9 | ENST00000313236.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM25 | ENST00000313236.10 | c.897G>A | p.Pro299= | synonymous_variant | 7/9 | 1 | NM_032780.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.272 AC: 41282AN: 151814Hom.: 6131 Cov.: 31
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GnomAD3 exomes AF: 0.302 AC: 75803AN: 251396Hom.: 13268 AF XY: 0.287 AC XY: 39058AN XY: 135870
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GnomAD4 exome AF: 0.288 AC: 420787AN: 1461796Hom.: 63812 Cov.: 46 AF XY: 0.283 AC XY: 205823AN XY: 727198
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GnomAD4 genome ? AF: 0.272 AC: 41334AN: 151934Hom.: 6150 Cov.: 31 AF XY: 0.272 AC XY: 20229AN XY: 74250
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at