chr15-48207506-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000338.3(SLC12A1):c.-186-28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 395,452 control chromosomes in the GnomAD database, including 3,140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.075 ( 1211 hom., cov: 32)
Exomes 𝑓: 0.047 ( 1929 hom. )
Consequence
SLC12A1
NM_000338.3 intron
NM_000338.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0450
Genes affected
SLC12A1 (HGNC:10910): (solute carrier family 12 member 1) This gene encodes a kidney-specific sodium-potassium-chloride cotransporter that is expressed on the luminal membrane of renal epithelial cells of the thick ascending limb of Henle's loop and the macula densa. It plays a key role in concentrating urine and accounts for most of the NaCl resorption. It is sensitive to such diuretics as furosemide and bumetanide. Some Bartter-like syndromes result from defects in this gene. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their biological validity in humans has not been experimentally proven.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 15-48207506-C-T is Benign according to our data. Variant chr15-48207506-C-T is described in ClinVar as [Benign]. Clinvar id is 1276462.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC12A1 | NM_000338.3 | c.-186-28C>T | intron_variant | ENST00000380993.8 | NP_000329.2 | |||
SLC12A1 | NM_001184832.2 | c.-186-28C>T | intron_variant | NP_001171761.1 | ||||
SLC12A1 | NM_001384136.1 | c.-186-28C>T | intron_variant | NP_001371065.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC12A1 | ENST00000380993.8 | c.-186-28C>T | intron_variant | 5 | NM_000338.3 | ENSP00000370381 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0747 AC: 11357AN: 152052Hom.: 1204 Cov.: 32
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GnomAD4 exome AF: 0.0466 AC: 11335AN: 243282Hom.: 1929 Cov.: 3 AF XY: 0.0452 AC XY: 5577AN XY: 123432
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GnomAD4 genome AF: 0.0748 AC: 11377AN: 152170Hom.: 1211 Cov.: 32 AF XY: 0.0771 AC XY: 5737AN XY: 74430
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 26, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at