1-1284044-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130413.4(SCNN1D):āc.418T>Cā(p.Trp140Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000187 in 1,335,154 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_001130413.4 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 |
---|---|---|---|---|---|---|---|
SCNN1D | NM_001130413.4 | c.418T>C | p.Trp140Arg | missense_variant | 5/18 | ENST00000379116.10 | |
SCNN1D | NR_037668.3 | n.644T>C | non_coding_transcript_exon_variant | 5/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1D | ENST00000379116.10 | c.418T>C | p.Trp140Arg | missense_variant | 5/18 | 5 | NM_001130413.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000228 AC: 2AN: 87830Hom.: 0 Cov.: 13
GnomAD3 exomes AF: 0.0000107 AC: 1AN: 93324Hom.: 0 AF XY: 0.0000188 AC XY: 1AN XY: 53316
GnomAD4 exome AF: 0.0000184 AC: 23AN: 1247324Hom.: 0 Cov.: 29 AF XY: 0.0000196 AC XY: 12AN XY: 612664
GnomAD4 genome ? AF: 0.0000228 AC: 2AN: 87830Hom.: 0 Cov.: 13 AF XY: 0.0000487 AC XY: 2AN XY: 41106
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.418T>C (p.W140R) alteration is located in exon 5 (coding exon 5) of the SCNN1D gene. This alteration results from a T to C substitution at nucleotide position 418, causing the tryptophan (W) at amino acid position 140 to be replaced by an arginine (R). 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