rs112530678
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001012755.5(SLC25A53):c.376G>T(p.Val126Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,210,107 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.
Frequency
Consequence
NM_001012755.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A53 | NM_001012755.5 | c.376G>T | p.Val126Leu | missense_variant | Exon 2 of 2 | ENST00000594199.3 | NP_001012773.2 | |
SLC25A53 | XM_005262129.6 | c.376G>T | p.Val126Leu | missense_variant | Exon 2 of 2 | XP_005262186.1 | ||
SLC25A53 | XM_011530952.4 | c.376G>T | p.Val126Leu | missense_variant | Exon 3 of 3 | XP_011529254.1 | ||
SLC25A53 | XM_011530953.4 | c.376G>T | p.Val126Leu | missense_variant | Exon 3 of 3 | XP_011529255.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000894 AC: 1AN: 111885Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34035
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183061Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67701
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1098222Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363582
GnomAD4 genome AF: 0.00000894 AC: 1AN: 111885Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34035
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at