rs10519974
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001046.3(SLC12A2):c.1409-887G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000658 in 151,928 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 𝑓 0.000066 ( 0 hom., cov: 32)
Consequence
SLC12A2
NM_001046.3 intron
NM_001046.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0290
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 -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A2 | NM_001046.3 | c.1409-887G>A | intron_variant | ENST00000262461.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A2 | ENST00000262461.7 | c.1409-887G>A | intron_variant | 1 | NM_001046.3 | P4 | |||
SLC12A2 | ENST00000343225.4 | c.1409-887G>A | intron_variant | 1 | A2 | ||||
SLC12A2 | ENST00000509205.5 | c.1409-887G>A | intron_variant, NMD_transcript_variant | 1 | |||||
SLC12A2 | ENST00000628403.2 | c.1409-887G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 151928Hom.: 0 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151928Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74192
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at