GeneBe

rs903498479

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_002457.5(MUC2):​c.4209T>A​(p.Thr1403Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T1403T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control

Consequence

MUC2
NM_002457.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

0 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP7
Synonymous conserved (PhyloP=-1.02 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.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MUC2
NM_002457.5
MANE Select
c.4209T>Ap.Thr1403Thr
synonymous
Exon 30 of 58NP_002448.5A0A3S8TMF2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MUC2
ENST00000361558.7
TSL:5
n.4236T>A
non_coding_transcript_exon
Exon 30 of 49
ENSG00000296903
ENST00000743440.1
n.141-131A>T
intron
N/A
MUC2
ENST00000675028.1
c.*27T>A
downstream_gene
N/AENSP00000502432.1A0A6Q8PGX3

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
136020
Hom.:
0
Cov.:
31
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
136124
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
66814
African (AFR)
AF:
0.00
AC:
0
AN:
36198
American (AMR)
AF:
0.00
AC:
0
AN:
14004
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3188
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4362
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4146
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9252
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
228
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
62094
Other (OTH)
AF:
0.00
AC:
0
AN:
1866
Alfa
AF:
0.0000530
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.062
DANN
Benign
0.14
PhyloP100
-1.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs903498479; hg19: chr11-1092390; API