rs13306676
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001126108.2(SLC12A3):c.2179-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,608,166 control chromosomes in the GnomAD database, including 13,540 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001126108.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A3 | NM_001126108.2 | c.2179-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000563236.6 | |||
SLC12A3 | NM_000339.3 | c.2179-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SLC12A3 | NM_001126107.2 | c.2176-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SLC12A3 | NM_001410896.1 | c.2176-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A3 | ENST00000563236.6 | c.2179-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001126108.2 | A1 | |||
SLC12A3 | ENST00000438926.6 | c.2179-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
SLC12A3 | ENST00000566786.5 | c.2176-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P4 | ||||
SLC12A3 | ENST00000262502.5 | c.2176-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.112 AC: 16781AN: 150388Hom.: 1085 Cov.: 28
GnomAD3 exomes AF: 0.127 AC: 31836AN: 250910Hom.: 2233 AF XY: 0.129 AC XY: 17508AN XY: 135764
GnomAD4 exome AF: 0.128 AC: 186225AN: 1457674Hom.: 12455 Cov.: 30 AF XY: 0.128 AC XY: 92773AN XY: 725314
GnomAD4 genome ? AF: 0.112 AC: 16788AN: 150492Hom.: 1085 Cov.: 28 AF XY: 0.114 AC XY: 8341AN XY: 73382
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Familial hypokalemia-hypomagnesemia Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 28, 2017 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 29, 2019 | This variant is associated with the following publications: (PMID: 28008009) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at