20-46051869-T-G
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_020708.5(SLC12A5):āc.2376T>Gā(p.Ile792Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.0 ( 0 hom., cov: 28)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC12A5
NM_020708.5 missense, splice_region
NM_020708.5 missense, splice_region
Scores
9
10
Splicing: ADA: 0.0001052
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.12
Genes affected
SLC12A5 (HGNC:13818): (solute carrier family 12 member 5) K-Cl cotransporters are proteins that lower intracellular chloride concentrations below the electrochemical equilibrium potential. The protein encoded by this gene is an integral membrane K-Cl cotransporter that can function in either a net efflux or influx pathway, depending on the chemical concentration gradients of potassium and chloride. The encoded protein can act as a homomultimer, or as a heteromultimer with other K-Cl cotransporters, to maintain chloride homeostasis in neurons. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.37809098).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC12A5 | NM_020708.5 | c.2376T>G | p.Ile792Met | missense_variant, splice_region_variant | Exon 18 of 26 | ENST00000243964.7 | NP_065759.1 | |
SLC12A5 | NM_001134771.2 | c.2445T>G | p.Ile815Met | missense_variant, splice_region_variant | Exon 18 of 26 | NP_001128243.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 115374Hom.: 0 Cov.: 28 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1092694Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 541454
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 115374Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 52758
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Benign
D;D
Sift4G
Uncertain
T;T
Polyphen
B;P
Vest4
MutPred
Gain of MoRF binding (P = 0.0778);.;
MVP
MPC
ClinPred
D
GERP RS
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gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at