rs796488792
Variant names:
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_002457.5(MUC2):c.4353C>T(p.Thr1451Thr) 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 0.000017 ( 0 hom., cov: 15)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MUC2
NM_002457.5 synonymous
NM_002457.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.09
Publications
0 publications found
Genes affected
MUC2 (HGNC:7512): (mucin 2, oligomeric mucus/gel-forming) This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. The protein polymerizes into a gel of which 80% is composed of oligosaccharide side chains by weight. The protein features a central domain containing tandem repeats rich in threonine and proline that varies between 50 and 115 copies in different individuals. Downregulation of this gene has been observed in patients with Crohn disease and ulcerative colitis. [provided by RefSeq, Oct 2016]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 11-1094596-C-T is Benign according to our data. Variant chr11-1094596-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2641130.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.09 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_002457.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MUC2 | NM_002457.5 | MANE Select | c.4353C>T | p.Thr1451Thr | synonymous | Exon 30 of 58 | NP_002448.5 | A0A3S8TMF2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MUC2 | ENST00000361558.7 | TSL:5 | n.4380C>T | non_coding_transcript_exon | Exon 30 of 49 | ||||
| ENSG00000296903 | ENST00000743440.1 | n.141-275G>A | intron | N/A | |||||
| MUC2 | ENST00000675028.1 | c.*171C>T | downstream_gene | N/A | ENSP00000502432.1 | A0A6Q8PGX3 |
Frequencies
GnomAD3 genomes 0.0000169 AC: 1AN: 59336Hom.: 0 Cov.: 15 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
59336
Hom.:
Cov.:
15
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000152 AC: 2AN: 1312684Hom.: 0 Cov.: 125 AF XY: 0.00 AC XY: 0AN XY: 642236 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2
AN:
1312684
Hom.:
Cov.:
125
AF XY:
AC XY:
0
AN XY:
642236
show subpopulations
African (AFR)
AF:
AC:
0
AN:
28502
American (AMR)
AF:
AC:
0
AN:
30658
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23324
East Asian (EAS)
AF:
AC:
0
AN:
31268
South Asian (SAS)
AF:
AC:
0
AN:
70292
European-Finnish (FIN)
AF:
AC:
0
AN:
40720
Middle Eastern (MID)
AF:
AC:
0
AN:
3830
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1030534
Other (OTH)
AF:
AC:
0
AN:
53556
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
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>80
Age
GnomAD4 genome 0.0000169 AC: 1AN: 59336Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0AN XY: 30320 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
59336
Hom.:
Cov.:
15
AF XY:
AC XY:
0
AN XY:
30320
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
16590
American (AMR)
AF:
AC:
0
AN:
7216
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1178
East Asian (EAS)
AF:
AC:
0
AN:
1518
South Asian (SAS)
AF:
AC:
0
AN:
1520
European-Finnish (FIN)
AF:
AC:
0
AN:
5672
Middle Eastern (MID)
AF:
AC:
0
AN:
130
European-Non Finnish (NFE)
AF:
AC:
1
AN:
24430
Other (OTH)
AF:
AC:
0
AN:
770
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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