chr12-6374399-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_001038.6(SCNN1A):c.385G>A(p.Ala129Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000415 in 1,614,054 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001038.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCNN1A | NM_001038.6 | c.385G>A | p.Ala129Thr | missense_variant | Exon 2 of 13 | ENST00000228916.7 | NP_001029.1 | |
SCNN1A | NM_001159576.2 | c.562G>A | p.Ala188Thr | missense_variant | Exon 1 of 12 | NP_001153048.1 | ||
SCNN1A | NM_001159575.2 | c.454G>A | p.Ala152Thr | missense_variant | Exon 2 of 13 | NP_001153047.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251302Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135882
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461866Hom.: 1 Cov.: 32 AF XY: 0.0000578 AC XY: 42AN XY: 727234
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Submissions by phenotype
Bronchiectasis with or without elevated sweat chloride 2 Uncertain:1
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Pseudohypoaldosteronism, type IB1, autosomal recessive Uncertain:1
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Bronchiectasis with or without elevated sweat chloride 2;C4748292:Liddle syndrome 3;C5774176:Pseudohypoaldosteronism, type IB1, autosomal recessive Uncertain:1
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not provided Uncertain:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at