chr20-46022977-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The ENST00000626701.1(SLC12A5):c.256A>G(p.Arg86Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 7/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.019 ( 1 hom., cov: 19)
Exomes 𝑓: 0.0010 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC12A5
ENST00000626701.1 missense
ENST00000626701.1 missense
Scores
9
Clinical Significance
Conservation
PhyloP100: 0.00
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 -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.13475034).
BP6
?
Variant 20-46022977-A-G is Benign according to our data. Variant chr20-46022977-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1686411.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A5 | NM_001134771.2 | c.121+1091A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A5 | ENST00000626701.1 | c.256A>G | p.Arg86Gly | missense_variant | 2/3 | 3 | |||
SLC12A5 | ENST00000413737.2 | c.97A>G | p.Arg33Gly | missense_variant | 2/3 | 3 | |||
SLC12A5 | ENST00000454036.6 | c.121+1091A>G | intron_variant | 5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1510AN: 79916Hom.: 1 Cov.: 19 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00103 AC: 175AN: 170292Hom.: 0 Cov.: 0 AF XY: 0.00127 AC XY: 111AN XY: 87460
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0189 AC: 1511AN: 79934Hom.: 1 Cov.: 19 AF XY: 0.0194 AC XY: 742AN XY: 38256
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
D
Sift4G
Benign
T
Vest4
MVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at