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GeneBe

11-1083094-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_002457.5(MUC2):c.1386C>T(p.Ser462=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,612,508 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0082 ( 6 hom., cov: 35)
Exomes 𝑓: 0.011 ( 93 hom. )

Consequence

MUC2
NM_002457.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.43
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 made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-1083094-C-T is Benign according to our data. Variant chr11-1083094-C-T is described in ClinVar as [Benign]. Clinvar id is 2641120.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.43 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MUC2NM_002457.5 linkuse as main transcriptc.1386C>T p.Ser462= synonymous_variant 11/58 ENST00000713550.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MUC2ENST00000675028.1 linkuse as main transcriptc.1386C>T p.Ser462= synonymous_variant 11/30 P3
MUC2ENST00000361558.7 linkuse as main transcriptn.1413C>T non_coding_transcript_exon_variant 11/495

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00819
AC:
1246
AN:
152212
Hom.:
5
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.00193
Gnomad AMI
AF:
0.0154
Gnomad AMR
AF:
0.00694
Gnomad ASJ
AF:
0.00432
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00662
Gnomad FIN
AF:
0.0227
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0110
Gnomad OTH
AF:
0.00431
GnomAD3 exomes
AF:
0.00904
AC:
2239
AN:
247752
Hom.:
16
AF XY:
0.00945
AC XY:
1275
AN XY:
134986
show subpopulations
Gnomad AFR exome
AF:
0.00163
Gnomad AMR exome
AF:
0.00412
Gnomad ASJ exome
AF:
0.00350
Gnomad EAS exome
AF:
0.000111
Gnomad SAS exome
AF:
0.00683
Gnomad FIN exome
AF:
0.0268
Gnomad NFE exome
AF:
0.0106
Gnomad OTH exome
AF:
0.00964
GnomAD4 exome
AF:
0.0106
AC:
15423
AN:
1460178
Hom.:
93
Cov.:
56
AF XY:
0.0104
AC XY:
7552
AN XY:
726352
show subpopulations
Gnomad4 AFR exome
AF:
0.00146
Gnomad4 AMR exome
AF:
0.00427
Gnomad4 ASJ exome
AF:
0.00463
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00697
Gnomad4 FIN exome
AF:
0.0265
Gnomad4 NFE exome
AF:
0.0112
Gnomad4 OTH exome
AF:
0.00936
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00821
AC:
1250
AN:
152330
Hom.:
6
Cov.:
35
AF XY:
0.00867
AC XY:
646
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.00190
Gnomad4 AMR
AF:
0.00693
Gnomad4 ASJ
AF:
0.00432
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00663
Gnomad4 FIN
AF:
0.0227
Gnomad4 NFE
AF:
0.0110
Gnomad4 OTH
AF:
0.00663
Alfa
AF:
0.00850
Hom.:
1
Bravo
AF:
0.00640
Asia WGS
AF:
0.00866
AC:
30
AN:
3478

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2023MUC2: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.031
Dann
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61732120; hg19: chr11-1081090; API