chr16-56893003-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001126108.2(SLC12A3):āc.2470T>Cā(p.Ser824Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S824T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001126108.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A3 | NM_001126108.2 | c.2470T>C | p.Ser824Pro | missense_variant | 21/26 | ENST00000563236.6 | |
SLC12A3 | NM_000339.3 | c.2497T>C | p.Ser833Pro | missense_variant | 21/26 | ||
SLC12A3 | NM_001126107.2 | c.2494T>C | p.Ser832Pro | missense_variant | 21/26 | ||
SLC12A3 | NM_001410896.1 | c.2467T>C | p.Ser823Pro | missense_variant | 21/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A3 | ENST00000563236.6 | c.2470T>C | p.Ser824Pro | missense_variant | 21/26 | 1 | NM_001126108.2 | A1 | |
SLC12A3 | ENST00000438926.6 | c.2497T>C | p.Ser833Pro | missense_variant | 21/26 | 1 | A1 | ||
SLC12A3 | ENST00000566786.5 | c.2494T>C | p.Ser832Pro | missense_variant | 21/26 | 1 | P4 | ||
SLC12A3 | ENST00000262502.5 | c.2467T>C | p.Ser823Pro | missense_variant | 21/26 | 5 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251062Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135762
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727230
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at