1-1281252-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001130413.4(SCNN1D):c.32C>T(p.Pro11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,535,590 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 Likely benign (★).
Frequency
Consequence
NM_001130413.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCNN1D | NM_001130413.4 | c.32C>T | p.Pro11Leu | missense_variant | 2/18 | ENST00000379116.10 | |
SCNN1D | NR_037668.3 | n.258C>T | non_coding_transcript_exon_variant | 2/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCNN1D | ENST00000379116.10 | c.32C>T | p.Pro11Leu | missense_variant | 2/18 | 5 | NM_001130413.4 | A2 | |
SCNN1D | ENST00000379101.8 | c.32C>T | p.Pro11Leu | missense_variant, NMD_transcript_variant | 2/17 | 1 | |||
SCNN1D | ENST00000338555.6 | c.-480C>T | 5_prime_UTR_variant | 1/15 | 2 | A2 | |||
SCNN1D | ENST00000400928.7 | c.-367C>T | 5_prime_UTR_variant | 1/16 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000744 AC: 1AN: 134496Hom.: 0 AF XY: 0.0000137 AC XY: 1AN XY: 73252
GnomAD4 exome AF: 0.0000275 AC: 38AN: 1383414Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 16AN XY: 682610
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at