1-1281479-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.146C>T(p.Thr49Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000262 in 1,524,488 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
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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.146C>T | p.Thr49Ile | missense_variant | 3/18 | ENST00000379116.10 | |
SCNN1D | NR_037668.3 | n.372C>T | non_coding_transcript_exon_variant | 3/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1D | ENST00000379116.10 | c.146C>T | p.Thr49Ile | missense_variant | 3/18 | 5 | NM_001130413.4 | A2 | |
SCNN1D | ENST00000379101.8 | c.146C>T | p.Thr49Ile | missense_variant, NMD_transcript_variant | 3/17 | 1 | |||
SCNN1D | ENST00000338555.6 | c.-253C>T | 5_prime_UTR_variant | 1/15 | 2 | A2 | |||
SCNN1D | ENST00000400928.7 | c.-253C>T | 5_prime_UTR_variant | 2/16 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152190Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000255 AC: 35AN: 1372180Hom.: 0 Cov.: 32 AF XY: 0.0000222 AC XY: 15AN XY: 676102
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 03, 2022 | The c.146C>T (p.T49I) 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 146, causing the threonine (T) at amino acid position 49 to be replaced by an isoleucine (I). 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