rs201433788
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_018406.7(MUC4):c.3718G>T(p.Ala1240Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.39 ( 183 hom., cov: 0)
Exomes 𝑓: 0.66 ( 81018 hom. )
Failed GnomAD Quality Control
Consequence
MUC4
NM_018406.7 missense
NM_018406.7 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: -3.35
Genes affected
MUC4 (HGNC:7514): (mucin 4, cell surface associated) The major constituents of mucus, the viscous secretion that covers epithelial surfaces such as those in the trachea, colon, and cervix, are highly glycosylated proteins called mucins. These glycoproteins play important roles in the protection of the epithelial cells and have been implicated in epithelial renewal and differentiation. This gene encodes an integral membrane glycoprotein found on the cell surface, although secreted isoforms may exist. At least two dozen transcript variants of this gene have been found, although for many of them the full-length transcript has not been determined or they are found only in tumor tissues. This gene contains a region in the coding sequence which has a variable number (>100) of 48 nt tandem repeats. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0016600192).
BP6
?
Variant 3-195787862-C-A is Benign according to our data. Variant chr3-195787862-C-A is described in ClinVar as [Benign]. Clinvar id is 403124.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC4 | NM_018406.7 | c.3718G>T | p.Ala1240Ser | missense_variant | 2/25 | ENST00000463781.8 | |
MUC4 | NM_004532.6 | c.83-9407G>T | intron_variant | ||||
MUC4 | NM_138297.5 | c.83-13557G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC4 | ENST00000463781.8 | c.3718G>T | p.Ala1240Ser | missense_variant | 2/25 | 5 | NM_018406.7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 890AN: 2274Hom.: 185 Cov.: 0 FAILED QC
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GnomAD3 exomes AF: 0.632 AC: 25717AN: 40662Hom.: 8738 AF XY: 0.629 AC XY: 13021AN XY: 20704
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.660 AC: 242133AN: 366850Hom.: 81018 Cov.: 4 AF XY: 0.658 AC XY: 126564AN XY: 192406
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.391 AC: 886AN: 2268Hom.: 183 Cov.: 0 AF XY: 0.387 AC XY: 416AN XY: 1076
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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 29, 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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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Vest4
ClinPred
T
gMVP
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