chr3-195750916-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018406.7(MUC4):c.15844G>A(p.Gly5282Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000914 in 1,613,776 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0048 ( 4 hom., cov: 29)
Exomes 𝑓: 0.00051 ( 3 hom. )
Consequence
MUC4
NM_018406.7 missense
NM_018406.7 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: 0.825
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 Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0031014085).
BP6
?
Variant 3-195750916-C-T is Benign according to our data. Variant chr3-195750916-C-T is described in ClinVar as [Benign]. Clinvar id is 708776.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUC4 | NM_018406.7 | c.15844G>A | p.Gly5282Arg | missense_variant | 23/25 | ENST00000463781.8 | |
MUC4 | NM_004532.6 | c.3136G>A | p.Gly1046Arg | missense_variant | 22/24 | ||
MUC4 | NM_138297.5 | c.2983G>A | p.Gly995Arg | missense_variant | 21/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUC4 | ENST00000463781.8 | c.15844G>A | p.Gly5282Arg | missense_variant | 23/25 | 5 | NM_018406.7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00481 AC: 732AN: 152086Hom.: 4 Cov.: 29
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00126 AC: 316AN: 251028Hom.: 1 AF XY: 0.000883 AC XY: 120AN XY: 135832
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GnomAD4 exome AF: 0.000508 AC: 742AN: 1461572Hom.: 3 Cov.: 37 AF XY: 0.000463 AC XY: 337AN XY: 727094
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GnomAD4 genome ? AF: 0.00482 AC: 733AN: 152204Hom.: 4 Cov.: 29 AF XY: 0.00445 AC XY: 331AN XY: 74412
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2018 | - - |
Computational scores
Source:
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;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
B;B;B;B
Vest4
MutPred
0.23
.;.;Gain of catalytic residue at G5282 (P = 0.0652);.;
MVP
ClinPred
T
GERP RS
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