rs6421972
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_002457.5(MUC2):c.10539C>A(p.Cys3513Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_002457.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC2 | NM_002457.5 | c.10539C>A | p.Cys3513Ter | stop_gained | 43/58 | ENST00000713550.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC2 | ENST00000674892.1 | c.1023C>A | p.Cys341Ter | stop_gained | 5/20 | A2 | |||
MUC2 | ENST00000361558.7 | n.10576C>A | non_coding_transcript_exon_variant | 34/49 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 34
GnomAD4 exome Cov.: 70
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152300Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74472
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at