10-99620215-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_031212.4(SLC25A28):c.121G>A(p.Ala41Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000488 in 1,394,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A41G) has been classified as Uncertain significance.
Frequency
Consequence
NM_031212.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000334 AC: 5AN: 149748Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000412 AC: 14AN: 34016Hom.: 0 AF XY: 0.000403 AC XY: 8AN XY: 19840
GnomAD4 exome AF: 0.0000506 AC: 63AN: 1244192Hom.: 0 Cov.: 34 AF XY: 0.0000707 AC XY: 43AN XY: 608548
GnomAD4 genome AF: 0.0000334 AC: 5AN: 149846Hom.: 0 Cov.: 32 AF XY: 0.0000410 AC XY: 3AN XY: 73114
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.121G>A (p.A41T) alteration is located in exon 1 (coding exon 1) of the SLC25A28 gene. This alteration results from a G to A substitution at nucleotide position 121, causing the alanine (A) at amino acid position 41 to be replaced by a threonine (T). 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