rs908229
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002458.3(MUC5B):āc.2007T>Cā(p.Tyr669=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,597,398 control chromosomes in the GnomAD database, including 213,100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.52 ( 20978 hom., cov: 35)
Exomes š: 0.51 ( 192122 hom. )
Consequence
MUC5B
NM_002458.3 synonymous
NM_002458.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.577
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 11-1232712-T-C is Benign according to our data. Variant chr11-1232712-T-C is described in ClinVar as [Benign]. Clinvar id is 163997.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC5B | NM_002458.3 | c.2007T>C | p.Tyr669= | synonymous_variant | 17/49 | ENST00000529681.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.2007T>C | p.Tyr669= | synonymous_variant | 17/49 | 5 | NM_002458.3 | P1 | |
MUC5B | ENST00000525715.5 | n.2065T>C | non_coding_transcript_exon_variant | 17/26 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.523 AC: 79434AN: 152014Hom.: 20955 Cov.: 35
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GnomAD4 exome AF: 0.514 AC: 742835AN: 1445266Hom.: 192122 Cov.: 69 AF XY: 0.513 AC XY: 367971AN XY: 717384
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GnomAD4 genome ? AF: 0.523 AC: 79503AN: 152132Hom.: 20978 Cov.: 35 AF XY: 0.529 AC XY: 39318AN XY: 74374
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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 | Feb 21, 2013 | Tyr669Tyr in exon 17 of MUC5B: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 40.0% (1720/4300) o f African American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs908229). - |
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