chr5-128084113-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001046.3(SLC12A2):c.159C>T(p.Gly53=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000765 in 1,306,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Consequence
SLC12A2
NM_001046.3 synonymous
NM_001046.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.293
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 Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 5-128084113-C-T is Benign according to our data. Variant chr5-128084113-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1568986.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.293 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A2 | NM_001046.3 | c.159C>T | p.Gly53= | synonymous_variant | 1/27 | ENST00000262461.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A2 | ENST00000262461.7 | c.159C>T | p.Gly53= | synonymous_variant | 1/27 | 1 | NM_001046.3 | P4 | |
SLC12A2 | ENST00000343225.4 | c.159C>T | p.Gly53= | synonymous_variant | 1/26 | 1 | A2 | ||
SLC12A2 | ENST00000509205.5 | c.159C>T | p.Gly53= | synonymous_variant, NMD_transcript_variant | 1/27 | 1 | |||
SLC12A2 | ENST00000628403.2 | c.159C>T | p.Gly53= | synonymous_variant | 1/26 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151566Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000692 AC: 8AN: 1155356Hom.: 0 Cov.: 30 AF XY: 0.0000125 AC XY: 7AN XY: 561512
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151566Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74006
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 10, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at