3-39383725-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_017875.4(SLC25A38):āc.1A>Gā(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017875.4 start_lost
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A38 | NM_017875.4 | c.1A>G | p.Met1? | start_lost | Exon 1 of 7 | ENST00000650617.1 | NP_060345.2 | |
SLC25A38 | NM_001354798.2 | c.1A>G | p.Met1? | start_lost | Exon 1 of 6 | NP_001341727.1 | ||
LOC105377644 | XR_007096252.1 | n.85+516T>C | intron_variant | Intron 1 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250950Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135778
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461736Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727170
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change affects the initiator methionine of the SLC25A38 mRNA. The next in-frame methionine is located at codon 23. This variant is present in population databases (rs765685556, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SLC25A38-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at