rs10089
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001046.3(SLC12A2):c.*220C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC12A2
NM_001046.3 3_prime_UTR
NM_001046.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.257
Genes affected
SLC12A2 (HGNC:10911): (solute carrier family 12 member 2) The protein encoded by this gene mediates sodium and chloride transport and reabsorption. The encoded protein is a membrane protein and is important in maintaining proper ionic balance and cell volume. This protein is phosphorylated in response to DNA damage. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A2 | NM_001046.3 | c.*220C>A | 3_prime_UTR_variant | 27/27 | ENST00000262461.7 | ||
SLC12A2 | NM_001256461.2 | c.*220C>A | 3_prime_UTR_variant | 26/26 | |||
SLC12A2 | NR_046207.2 | n.4114C>A | non_coding_transcript_exon_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A2 | ENST00000262461.7 | c.*220C>A | 3_prime_UTR_variant | 27/27 | 1 | NM_001046.3 | P4 | ||
SLC12A2 | ENST00000343225.4 | c.*220C>A | 3_prime_UTR_variant | 26/26 | 1 | A2 | |||
SLC12A2 | ENST00000509205.5 | c.*472C>A | 3_prime_UTR_variant, NMD_transcript_variant | 27/27 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 250324Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0AN XY: 128594
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
250324
Hom.:
Cov.:
4
AF XY:
AC XY:
0
AN XY:
128594
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at