NM_004277.5:c.169C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004277.5(SLC25A27):c.169C>T(p.Arg57Trp) 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 1,613,504 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R57P) has been classified as Uncertain significance.
Frequency
Consequence
NM_004277.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A27 | ENST00000371347.10 | c.169C>T | p.Arg57Trp | missense_variant | Exon 2 of 9 | 1 | NM_004277.5 | ENSP00000360398.3 | ||
SLC25A27 | ENST00000411689.6 | c.169C>T | p.Arg57Trp | missense_variant | Exon 2 of 7 | 1 | ENSP00000412024.2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151900Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249130Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135198
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461604Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727108
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151900Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74156
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.169C>T (p.R57W) alteration is located in exon 2 (coding exon 2) of the SLC25A27 gene. This alteration results from a C to T substitution at nucleotide position 169, causing the arginine (R) at amino acid position 57 to be replaced by a tryptophan (W). 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