chr3-125083942-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024628.6(SLC12A8):c.2093G>A(p.Arg698His) variant causes a missense change. The variant allele was found at a frequency of 0.0000347 in 1,613,406 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R698P) has been classified as Uncertain significance.
Frequency
Consequence
NM_024628.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A8 | NM_024628.6 | c.2093G>A | p.Arg698His | missense_variant | 14/14 | ENST00000469902.6 | |
SLC12A8 | NM_001195483.2 | c.2093G>A | p.Arg698His | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A8 | ENST00000469902.6 | c.2093G>A | p.Arg698His | missense_variant | 14/14 | 2 | NM_024628.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151950Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 248064Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134546
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461456Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 726970
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151950Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74186
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 25, 2024 | The c.2093G>A (p.R698H) alteration is located in exon 14 (coding exon 13) of the SLC12A8 gene. This alteration results from a G to A substitution at nucleotide position 2093, causing the arginine (R) at amino acid position 698 to be replaced by a histidine (H). 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