1-1281527-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130413.4(SCNN1D):c.194C>T(p.Pro65Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000391 in 1,535,524 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 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
Genome browser will be placed here
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.194C>T | p.Pro65Leu | missense_variant | 3/18 | ENST00000379116.10 | |
SCNN1D | NR_037668.3 | n.420C>T | non_coding_transcript_exon_variant | 3/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1D | ENST00000379116.10 | c.194C>T | p.Pro65Leu | missense_variant | 3/18 | 5 | NM_001130413.4 | A2 | |
SCNN1D | ENST00000379101.8 | c.194C>T | p.Pro65Leu | missense_variant, NMD_transcript_variant | 3/17 | 1 | |||
SCNN1D | ENST00000338555.6 | c.-205C>T | 5_prime_UTR_variant | 1/15 | 2 | A2 | |||
SCNN1D | ENST00000400928.7 | c.-205C>T | 5_prime_UTR_variant | 2/16 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000747 AC: 1AN: 133920Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 72880
GnomAD4 exome AF: 0.00000289 AC: 4AN: 1383300Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 682546
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.194C>T (p.P65L) alteration is located in exon 3 (coding exon 3) of the SCNN1D gene. This alteration results from a C to T substitution at nucleotide position 194, causing the proline (P) at amino acid position 65 to be replaced by a leucine (L). 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