rs5801
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001126108.2(SLC12A3):c.1395C>A(p.Thr465=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,454 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T465T) has been classified as Benign.
Frequency
Consequence
NM_001126108.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A3 | NM_001126108.2 | c.1395C>A | p.Thr465= | synonymous_variant | 11/26 | ENST00000563236.6 | |
SLC12A3 | NM_000339.3 | c.1395C>A | p.Thr465= | synonymous_variant | 11/26 | ||
SLC12A3 | NM_001126107.2 | c.1392C>A | p.Thr464= | synonymous_variant | 11/26 | ||
SLC12A3 | NM_001410896.1 | c.1392C>A | p.Thr464= | synonymous_variant | 11/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A3 | ENST00000563236.6 | c.1395C>A | p.Thr465= | synonymous_variant | 11/26 | 1 | NM_001126108.2 | A1 | |
SLC12A3 | ENST00000438926.6 | c.1395C>A | p.Thr465= | synonymous_variant | 11/26 | 1 | A1 | ||
SLC12A3 | ENST00000566786.5 | c.1392C>A | p.Thr464= | synonymous_variant | 11/26 | 1 | P4 | ||
SLC12A3 | ENST00000262502.5 | c.1392C>A | p.Thr464= | synonymous_variant | 11/26 | 5 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251014Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135764
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461454Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727076
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 01, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at