rs200696532
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001135091.2(MUC15):c.946C>T(p.Pro316Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,609,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. P316T) has been classified as Uncertain significance.
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUC15 | NM_001135091.2 | c.946C>T | p.Pro316Ser | missense_variant | Exon 5 of 5 | ENST00000529533.6 | NP_001128563.1 | |
ANO3 | NM_031418.4 | c.1447+1426G>A | intron_variant | Intron 14 of 26 | ENST00000256737.8 | NP_113606.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUC15 | ENST00000529533.6 | c.946C>T | p.Pro316Ser | missense_variant | Exon 5 of 5 | 1 | NM_001135091.2 | ENSP00000431983.1 | ||
ANO3 | ENST00000256737.8 | c.1447+1426G>A | intron_variant | Intron 14 of 26 | 1 | NM_031418.4 | ENSP00000256737.3 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151940Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 57AN: 246780Hom.: 1 AF XY: 0.000262 AC XY: 35AN XY: 133540
GnomAD4 exome AF: 0.0000439 AC: 64AN: 1457354Hom.: 0 Cov.: 30 AF XY: 0.0000483 AC XY: 35AN XY: 724908
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74324
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at