11-1191741-C-T
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001304359.2(MUC5AC):c.13596C>T(p.Ala4532Ala) 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MUC5AC
NM_001304359.2 synonymous
NM_001304359.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.34
Genes affected
MUC5AC (HGNC:7515): (mucin 5AC, oligomeric mucus/gel-forming) Predicted to be an extracellular matrix structural constituent. Involved in phosphatidylinositol-mediated signaling. Located in cytoplasm; extracellular space; and mucus layer. Implicated in dry eye syndrome. Biomarker of several diseases, including Sjogren's syndrome; biliary tract disease (multiple); cystic fibrosis; eye disease (multiple); and pancreatic cancer (multiple). [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.82).
BP6
Variant 11-1191741-C-T is Benign according to our data. Variant chr11-1191741-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641166.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.34 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MUC5AC | NM_001304359.2 | c.13596C>T | p.Ala4532Ala | synonymous_variant | 31/49 | ENST00000621226.2 | NP_001291288.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MUC5AC | ENST00000621226.2 | c.13596C>T | p.Ala4532Ala | synonymous_variant | 31/49 | 5 | NM_001304359.2 | ENSP00000485659.1 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 128002Hom.: 0 Cov.: 27 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 584302Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 318734
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GnomAD4 genome 0.00 AC: 0AN: 128002Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 62012
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | MUC5AC: BP4, BP7 - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at