rs4963056
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_002458.3(MUC5B):c.11517C>T(p.Thr3839=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,610,678 control chromosomes in the GnomAD database, including 82,438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.29 ( 7216 hom., cov: 28)
Exomes 𝑓: 0.31 ( 75222 hom. )
Consequence
MUC5B
NM_002458.3 synonymous
NM_002458.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.75
Genes affected
MUC5B (HGNC:7516): (mucin 5B, oligomeric mucus/gel-forming) This gene encodes a member of the mucin family of proteins, which are highly glycosylated macromolecular components of mucus secretions. This family member is the major gel-forming mucin in mucus. It is a major contributor to the lubricating and viscoelastic properties of whole saliva, normal lung mucus and cervical mucus. This gene has been found to be up-regulated in some human diseases, including sinus mucosa of chronic rhinosinusitis (CRS), CRS with nasal polyposis, chronic obstructive pulmonary disease (COPD) and H. pylori-associated gastric disease, and it may be involved in the pathogenesis of these diseases. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 11-1248397-C-T is Benign according to our data. Variant chr11-1248397-C-T is described in ClinVar as [Benign]. Clinvar id is 403168.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
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Synonymous conserved (PhyloP=-3.75 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC5B | NM_002458.3 | c.11517C>T | p.Thr3839= | synonymous_variant | 31/49 | ENST00000529681.5 | |
MUC5B-AS1 | NR_157183.1 | n.56+1224G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.11517C>T | p.Thr3839= | synonymous_variant | 31/49 | 5 | NM_002458.3 | P1 | |
MUC5B-AS1 | ENST00000532061.2 | n.56+1224G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.294 AC: 44043AN: 149726Hom.: 7202 Cov.: 28
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GnomAD3 exomes AF: 0.321 AC: 79898AN: 248846Hom.: 13871 AF XY: 0.320 AC XY: 43182AN XY: 135050
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GnomAD4 exome AF: 0.314 AC: 458103AN: 1460832Hom.: 75222 Cov.: 150 AF XY: 0.312 AC XY: 226727AN XY: 726688
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GnomAD4 genome ? AF: 0.294 AC: 44076AN: 149846Hom.: 7216 Cov.: 28 AF XY: 0.295 AC XY: 21619AN XY: 73168
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
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 - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
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