rs11245936
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP3BA1
The NM_002457.5(MUC2):c.2494G>A(p.Gly832Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0823 in 1,613,088 control chromosomes in the GnomAD database, including 5,881 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.070 ( 413 hom., cov: 33)
Exomes 𝑓: 0.084 ( 5468 hom. )
Consequence
MUC2
NM_002457.5 missense
NM_002457.5 missense
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.59
Genes affected
MUC2 (HGNC:7512): (mucin 2, oligomeric mucus/gel-forming) This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. The protein polymerizes into a gel of which 80% is composed of oligosaccharide side chains by weight. The protein features a central domain containing tandem repeats rich in threonine and proline that varies between 50 and 115 copies in different individuals. Downregulation of this gene has been observed in patients with Crohn disease and ulcerative colitis. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC2 | NM_002457.5 | c.2494G>A | p.Gly832Ser | missense_variant | 19/58 | ENST00000713550.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC2 | ENST00000675028.1 | c.2494G>A | p.Gly832Ser | missense_variant | 19/30 | P3 | |||
MUC2 | ENST00000361558.7 | n.2521G>A | non_coding_transcript_exon_variant | 19/49 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0696 AC: 10593AN: 152124Hom.: 413 Cov.: 33
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GnomAD3 exomes AF: 0.0706 AC: 17500AN: 247974Hom.: 706 AF XY: 0.0710 AC XY: 9578AN XY: 134982
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GnomAD4 exome AF: 0.0836 AC: 122186AN: 1460846Hom.: 5468 Cov.: 34 AF XY: 0.0828 AC XY: 60154AN XY: 726688
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GnomAD4 genome ? AF: 0.0696 AC: 10596AN: 152242Hom.: 413 Cov.: 33 AF XY: 0.0695 AC XY: 5173AN XY: 74422
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Not reported inComputational scores
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DS_AG_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at