chr3-125083915-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024628.6(SLC12A8):c.2120G>A(p.Arg707Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,612,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024628.6 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 | UniProt |
---|---|---|---|---|---|---|---|
SLC12A8 | NM_024628.6 | c.2120G>A | p.Arg707Gln | missense_variant | 14/14 | ENST00000469902.6 | |
SLC12A8 | NM_001195483.2 | c.2120G>A | p.Arg707Gln | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A8 | ENST00000469902.6 | c.2120G>A | p.Arg707Gln | missense_variant | 14/14 | 2 | NM_024628.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 151924Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000445 AC: 11AN: 247182Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134050
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460986Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726648
GnomAD4 genome AF: 0.0000592 AC: 9AN: 151924Hom.: 0 Cov.: 31 AF XY: 0.0000809 AC XY: 6AN XY: 74164
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.2120G>A (p.R707Q) 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 2120, causing the arginine (R) at amino acid position 707 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