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11-1082921-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_002457.5(MUC2):c.1301C>G(p.Pro434Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,612,678 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 2 hom., cov: 35)
Exomes 𝑓: 0.0046 ( 25 hom. )

Consequence

MUC2
NM_002457.5 missense

Scores

1
1

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.614
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 -8 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=-0.31).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-1082921-C-G is Benign according to our data. Variant chr11-1082921-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3024844.Status of the report is criteria_provided_single_submitter, 1 stars.
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 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MUC2NM_002457.5 linkuse as main transcriptc.1301C>G p.Pro434Arg missense_variant 10/58 ENST00000713550.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MUC2ENST00000675028.1 linkuse as main transcriptc.1301C>G p.Pro434Arg missense_variant 10/30 P3
MUC2ENST00000361558.7 linkuse as main transcriptn.1328C>G non_coding_transcript_exon_variant 10/495

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00317
AC:
482
AN:
152214
Hom.:
2
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.000772
Gnomad AMI
AF:
0.0164
Gnomad AMR
AF:
0.00105
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00226
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00553
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00340
AC:
844
AN:
248154
Hom.:
4
AF XY:
0.00345
AC XY:
466
AN XY:
135074
show subpopulations
Gnomad AFR exome
AF:
0.00137
Gnomad AMR exome
AF:
0.000754
Gnomad ASJ exome
AF:
0.00130
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00141
Gnomad FIN exome
AF:
0.00195
Gnomad NFE exome
AF:
0.00607
Gnomad OTH exome
AF:
0.00298
GnomAD4 exome
AF:
0.00458
AC:
6686
AN:
1460346
Hom.:
25
Cov.:
35
AF XY:
0.00451
AC XY:
3274
AN XY:
726426
show subpopulations
Gnomad4 AFR exome
AF:
0.000687
Gnomad4 AMR exome
AF:
0.000604
Gnomad4 ASJ exome
AF:
0.00145
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00146
Gnomad4 FIN exome
AF:
0.00207
Gnomad4 NFE exome
AF:
0.00548
Gnomad4 OTH exome
AF:
0.00454
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00316
AC:
482
AN:
152332
Hom.:
2
Cov.:
35
AF XY:
0.00301
AC XY:
224
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.000769
Gnomad4 AMR
AF:
0.00105
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.00226
Gnomad4 NFE
AF:
0.00553
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00155
Hom.:
0
Bravo
AF:
0.00274
EpiCase
AF:
0.00469
EpiControl
AF:
0.00415

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 TuebingenFeb 01, 2024MUC2: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.31
Cadd
Benign
17
Dann
Uncertain
0.99

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

LitVar

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

Other links and lift over

dbSNP: rs41442048; hg19: chr11-1080917; API