rs79635145
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001164462.2(MUC12):c.13695C>T(p.Ser4565=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.57 ( 473 hom., cov: 3)
Exomes 𝑓: 0.64 ( 83552 hom. )
Failed GnomAD Quality Control
Consequence
MUC12
NM_001164462.2 synonymous
NM_001164462.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.91
Genes affected
MUC12 (HGNC:7510): (mucin 12, cell surface associated) This gene encodes an integral membrane glycoprotein that is a member of the mucin family. Mucins are O-glycosylated proteins that play an essential role in forming protective mucous barriers on epithelial surfaces and have been implicated in epithelial renewal and differentiation. These glycoproteins also play a role in intracellular signaling. This protein is expressed on the apical membrane surface of epithelial cells that line the mucosal surfaces of many different tissues including the colon, pancreas, prostate, and uterus. The expression of this gene is downregulated in colorectal cancer tissue. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
?
Variant 7-101004258-C-T is Benign according to our data. Variant chr7-101004258-C-T is described in ClinVar as [Benign]. Clinvar id is 403116.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.91 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC12 | NM_001164462.2 | c.13695C>T | p.Ser4565= | synonymous_variant | 2/12 | ENST00000536621.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC12 | ENST00000536621.6 | c.13695C>T | p.Ser4565= | synonymous_variant | 2/12 | 5 | NM_001164462.2 | A2 | |
MUC12 | ENST00000379442.7 | c.14124C>T | p.Ser4708= | synonymous_variant | 5/15 | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1191AN: 2086Hom.: 473 Cov.: 3 FAILED QC
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GnomAD3 exomes AF: 0.751 AC: 40691AN: 54170Hom.: 15365 AF XY: 0.752 AC XY: 20455AN XY: 27194
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.636 AC: 283155AN: 445316Hom.: 83552 Cov.: 7 AF XY: 0.636 AC XY: 143557AN XY: 225548
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.572 AC: 1193AN: 2084Hom.: 473 Cov.: 3 AF XY: 0.563 AC XY: 526AN XY: 934
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at