rs2856111
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_002457.5(MUC2):c.173C>T(p.Pro58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 1,609,964 control chromosomes in the GnomAD database, including 581,143 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.79 ( 48650 hom., cov: 35)
Exomes 𝑓: 0.85 ( 532493 hom. )
Consequence
MUC2
NM_002457.5 missense
NM_002457.5 missense
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.903
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 -8 ACMG points.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUC2 | NM_002457.5 | c.173C>T | p.Pro58Leu | missense_variant | 2/58 | ENST00000713550.1 | NP_002448.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUC2 | ENST00000675028.1 | c.173C>T | p.Pro58Leu | missense_variant | 2/30 | ENSP00000502432 | P3 | |||
MUC2 | ENST00000361558.7 | n.200C>T | non_coding_transcript_exon_variant | 2/49 | 5 |
Frequencies
GnomAD3 genomes AF: 0.791 AC: 120367AN: 152094Hom.: 48625 Cov.: 35
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GnomAD4 exome AF: 0.852 AC: 1242079AN: 1457750Hom.: 532493 Cov.: 75 AF XY: 0.852 AC XY: 617823AN XY: 724918
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GnomAD4 genome AF: 0.791 AC: 120452AN: 152214Hom.: 48650 Cov.: 35 AF XY: 0.790 AC XY: 58807AN XY: 74424
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Uncertain
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at