8-103414823-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_030780.5(SLC25A32):c.115G>T(p.Ala39Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000899 in 1,613,698 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A39V) has been classified as Uncertain significance.
Frequency
Consequence
NM_030780.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A32 | NM_030780.5 | c.115G>T | p.Ala39Ser | missense_variant | 1/7 | ENST00000297578.9 | |
SLC25A32 | NR_102337.2 | n.285G>T | non_coding_transcript_exon_variant | 1/6 | |||
SLC25A32 | NR_102338.2 | n.285G>T | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A32 | ENST00000297578.9 | c.115G>T | p.Ala39Ser | missense_variant | 1/7 | 1 | NM_030780.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000124 AC: 31AN: 250154Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135636
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461462Hom.: 0 Cov.: 32 AF XY: 0.0000990 AC XY: 72AN XY: 727048
GnomAD4 genome AF: 0.000112 AC: 17AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74374
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at