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GeneBe

11-1086284-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.2412C>T(p.Asp804=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,612,000 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 11 hom. )

Consequence

MUC2
NM_002457.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.84
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=-0.96).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-1086284-C-T is Benign according to our data. Variant chr11-1086284-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641124.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=-4.84 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 GnomAdExome at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MUC2NM_002457.5 linkuse as main transcriptc.2412C>T p.Asp804= synonymous_variant 19/58 ENST00000713550.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MUC2ENST00000675028.1 linkuse as main transcriptc.2412C>T p.Asp804= synonymous_variant 19/30 P3
MUC2ENST00000361558.7 linkuse as main transcriptn.2439C>T non_coding_transcript_exon_variant 19/495

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00112
AC:
170
AN:
152220
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000458
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000827
Gnomad FIN
AF:
0.000659
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00191
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00130
AC:
318
AN:
245296
Hom.:
3
AF XY:
0.00132
AC XY:
177
AN XY:
133708
show subpopulations
Gnomad AFR exome
AF:
0.000535
Gnomad AMR exome
AF:
0.000410
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000561
Gnomad SAS exome
AF:
0.000594
Gnomad FIN exome
AF:
0.00136
Gnomad NFE exome
AF:
0.00218
Gnomad OTH exome
AF:
0.00101
GnomAD4 exome
AF:
0.00181
AC:
2644
AN:
1459662
Hom.:
11
Cov.:
32
AF XY:
0.00183
AC XY:
1325
AN XY:
726028
show subpopulations
Gnomad4 AFR exome
AF:
0.000269
Gnomad4 AMR exome
AF:
0.000449
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.000535
Gnomad4 FIN exome
AF:
0.00147
Gnomad4 NFE exome
AF:
0.00216
Gnomad4 OTH exome
AF:
0.00144
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00112
AC:
170
AN:
152338
Hom.:
0
Cov.:
33
AF XY:
0.000899
AC XY:
67
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.000457
Gnomad4 AMR
AF:
0.000457
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000828
Gnomad4 FIN
AF:
0.000659
Gnomad4 NFE
AF:
0.00191
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00133
Hom.:
0
Bravo
AF:
0.00109

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2023MUC2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.42
Dann
Benign
0.87

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs61732127; hg19: chr11-1084280; API