rs293979
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001135091.2(MUC15):c.137C>T(p.Ser46Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,611,394 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S46W) has been classified as Likely benign.
Frequency
Consequence
NM_001135091.2 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 |
---|---|---|---|---|---|---|---|
MUC15 | NM_001135091.2 | c.137C>T | p.Ser46Leu | missense_variant | 3/5 | ENST00000529533.6 | |
ANO3 | NM_031418.4 | c.1447+6024G>A | intron_variant | ENST00000256737.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC15 | ENST00000529533.6 | c.137C>T | p.Ser46Leu | missense_variant | 3/5 | 1 | NM_001135091.2 | ||
ANO3 | ENST00000256737.8 | c.1447+6024G>A | intron_variant | 1 | NM_031418.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000400 AC: 6AN: 150182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250414Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135350
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461094Hom.: 0 Cov.: 34 AF XY: 0.0000165 AC XY: 12AN XY: 726846
GnomAD4 genome ? AF: 0.0000399 AC: 6AN: 150300Hom.: 0 Cov.: 33 AF XY: 0.0000272 AC XY: 2AN XY: 73558
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at