4-127764245-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_031291.4(SLC25A31):c.363C>T(p.Phe121Phe) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,460,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_031291.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A31 | NM_031291.4 | c.363C>T | p.Phe121Phe | splice_region_variant, synonymous_variant | Exon 3 of 6 | ENST00000281154.6 | NP_112581.1 | |
SLC25A31 | NM_001318467.2 | c.363C>T | p.Phe121Phe | splice_region_variant, synonymous_variant | Exon 3 of 7 | NP_001305396.1 | ||
SLC25A31 | XM_011532298.3 | c.361-4507C>T | intron_variant | Intron 2 of 3 | XP_011530600.1 | |||
LOC105377414 | XR_939188.3 | n.565-707G>A | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250644Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135512
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460220Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726484
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at