rs56141203
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002458.3(MUC5B):c.15478-13T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,607,834 control chromosomes in the GnomAD database, including 895 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.025 ( 63 hom., cov: 33)
Exomes 𝑓: 0.030 ( 832 hom. )
Consequence
MUC5B
NM_002458.3 splice_polypyrimidine_tract, intron
NM_002458.3 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.11
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=-0.91).
BP6
?
Variant 11-1254681-T-C is Benign according to our data. Variant chr11-1254681-T-C is described in ClinVar as [Benign]. Clinvar id is 164003.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-1254681-T-C is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.025 (3807/152314) while in subpopulation NFE AF= 0.0328 (2228/68014). AF 95% confidence interval is 0.0316. There are 63 homozygotes in gnomad4. There are 1892 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 3808 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC5B | NM_002458.3 | c.15478-13T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000529681.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC5B | ENST00000529681.5 | c.15478-13T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_002458.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0250 AC: 3808AN: 152196Hom.: 63 Cov.: 33
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GnomAD3 exomes AF: 0.0266 AC: 6521AN: 245246Hom.: 135 AF XY: 0.0265 AC XY: 3535AN XY: 133616
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GnomAD4 exome AF: 0.0301 AC: 43781AN: 1455520Hom.: 832 Cov.: 34 AF XY: 0.0294 AC XY: 21278AN XY: 723154
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GnomAD4 genome ? AF: 0.0250 AC: 3807AN: 152314Hom.: 63 Cov.: 33 AF XY: 0.0254 AC XY: 1892AN XY: 74468
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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 | 15478-13T>C in intron 34 of MUC5B: This variant is not expected to have clinical significance because it has been identified in 3.0% (253/8296) of European Amer ican chromosomes from a broad population by the NHLBI Exome Sequencing Project ( http://evs.gs.washington.edu/EVS; dbSNP rs56141203). - |
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