4-127773401-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031291.4(SLC25A31):c.775C>T(p.Arg259Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,611,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031291.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A31 | NM_031291.4 | c.775C>T | p.Arg259Trp | missense_variant | Exon 6 of 6 | ENST00000281154.6 | NP_112581.1 | |
SLC25A31 | XM_011532298.3 | c.502C>T | p.Arg168Trp | missense_variant | Exon 4 of 4 | XP_011530600.1 | ||
SLC25A31 | NM_001318467.2 | c.*8C>T | 3_prime_UTR_variant | Exon 7 of 7 | NP_001305396.1 | |||
LOC105377414 | XR_939188.3 | n.564+2266G>A | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249360Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134796
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1459868Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 726172
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152064Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.775C>T (p.R259W) alteration is located in exon 6 (coding exon 6) of the SLC25A31 gene. This alteration results from a C to T substitution at nucleotide position 775, causing the arginine (R) at amino acid position 259 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