rs2228576
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001038.6(SCNN1A):c.1987A>T(p.Thr663Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,446,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T663A) has been classified as Benign.
Frequency
Consequence
NM_001038.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCNN1A | NM_001038.6 | c.1987A>T | p.Thr663Ser | missense_variant | 13/13 | ENST00000228916.7 | |
SCNN1A | NM_001159576.2 | c.2164A>T | p.Thr722Ser | missense_variant | 12/12 | ||
SCNN1A | NM_001159575.2 | c.2056A>T | p.Thr686Ser | missense_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1A | ENST00000228916.7 | c.1987A>T | p.Thr663Ser | missense_variant | 13/13 | 1 | NM_001038.6 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000451 AC: 1AN: 221868Hom.: 0 AF XY: 0.00000824 AC XY: 1AN XY: 121296
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1446050Hom.: 0 Cov.: 41 AF XY: 0.00000279 AC XY: 2AN XY: 718096
GnomAD4 genome ? Cov.: 34
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at