rs143714318
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001126108.2(SLC12A3):c.450T>A(p.Ile150=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,954 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. I150I) has been classified as Likely 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.450T>A | p.Ile150= | synonymous_variant | 3/26 | ENST00000563236.6 | |
SLC12A3 | NM_000339.3 | c.450T>A | p.Ile150= | synonymous_variant | 3/26 | ||
SLC12A3 | NM_001126107.2 | c.447T>A | p.Ile149= | synonymous_variant | 3/26 | ||
SLC12A3 | NM_001410896.1 | c.447T>A | p.Ile149= | synonymous_variant | 3/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A3 | ENST00000563236.6 | c.450T>A | p.Ile150= | synonymous_variant | 3/26 | 1 | NM_001126108.2 | A1 | |
SLC12A3 | ENST00000438926.6 | c.450T>A | p.Ile150= | synonymous_variant | 3/26 | 1 | A1 | ||
SLC12A3 | ENST00000566786.5 | c.447T>A | p.Ile149= | synonymous_variant | 3/26 | 1 | P4 | ||
SLC12A3 | ENST00000262502.5 | c.447T>A | p.Ile149= | synonymous_variant | 3/26 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250816Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135606
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461732Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727130
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at