13-45398989-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010875.4(SLC25A30):c.704G>A(p.Arg235Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,613,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010875.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A30 | NM_001010875.4 | c.704G>A | p.Arg235Gln | missense_variant | 8/10 | ENST00000519676.6 | NP_001010875.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A30 | ENST00000519676.6 | c.704G>A | p.Arg235Gln | missense_variant | 8/10 | 1 | NM_001010875.4 | ENSP00000429168.1 |
Frequencies
GnomAD3 genomes AF: 0.000178 AC: 27AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251448Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135896
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461854Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 727232
GnomAD4 genome AF: 0.000178 AC: 27AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.704G>A (p.R235Q) alteration is located in exon 8 (coding exon 7) of the SLC25A30 gene. This alteration results from a G to A substitution at nucleotide position 704, causing the arginine (R) at amino acid position 235 to be replaced by a glutamine (Q). 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