1-1284017-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001130413.4(SCNN1D):c.391C>T(p.Pro131Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 1,435,400 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130413.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCNN1D | NM_001130413.4 | c.391C>T | p.Pro131Ser | missense_variant | 5/18 | ENST00000379116.10 | |
SCNN1D | NR_037668.3 | n.617C>T | non_coding_transcript_exon_variant | 5/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1D | ENST00000379116.10 | c.391C>T | p.Pro131Ser | missense_variant | 5/18 | 5 | NM_001130413.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000385 AC: 5AN: 129932Hom.: 0 Cov.: 23
GnomAD3 exomes AF: 0.0000316 AC: 3AN: 94970Hom.: 0 AF XY: 0.0000372 AC XY: 2AN XY: 53828
GnomAD4 exome AF: 0.0000299 AC: 39AN: 1305364Hom.: 2 Cov.: 29 AF XY: 0.0000311 AC XY: 20AN XY: 642182
GnomAD4 genome AF: 0.0000385 AC: 5AN: 130036Hom.: 0 Cov.: 23 AF XY: 0.0000321 AC XY: 2AN XY: 62308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.391C>T (p.P131S) alteration is located in exon 5 (coding exon 5) of the SCNN1D gene. This alteration results from a C to T substitution at nucleotide position 391, causing the proline (P) at amino acid position 131 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at