rs2856111

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002457.5(MUC2):​c.173C>T​(p.Pro58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 1,609,964 control chromosomes in the GnomAD database, including 581,143 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.79 ( 48650 hom., cov: 35)
Exomes 𝑓: 0.85 ( 532493 hom. )

Consequence

MUC2
NM_002457.5 missense

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.903
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.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MUC2NM_002457.5 linkuse as main transcriptc.173C>T p.Pro58Leu missense_variant 2/58 ENST00000713550.1 NP_002448.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MUC2ENST00000675028.1 linkuse as main transcriptc.173C>T p.Pro58Leu missense_variant 2/30 ENSP00000502432 P3
MUC2ENST00000361558.7 linkuse as main transcriptn.200C>T non_coding_transcript_exon_variant 2/495

Frequencies

GnomAD3 genomes
AF:
0.791
AC:
120367
AN:
152094
Hom.:
48625
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.637
Gnomad AMI
AF:
0.872
Gnomad AMR
AF:
0.863
Gnomad ASJ
AF:
0.880
Gnomad EAS
AF:
0.532
Gnomad SAS
AF:
0.838
Gnomad FIN
AF:
0.825
Gnomad MID
AF:
0.889
Gnomad NFE
AF:
0.873
Gnomad OTH
AF:
0.828
GnomAD4 exome
AF:
0.852
AC:
1242079
AN:
1457750
Hom.:
532493
Cov.:
75
AF XY:
0.852
AC XY:
617823
AN XY:
724918
show subpopulations
Gnomad4 AFR exome
AF:
0.625
Gnomad4 AMR exome
AF:
0.891
Gnomad4 ASJ exome
AF:
0.872
Gnomad4 EAS exome
AF:
0.530
Gnomad4 SAS exome
AF:
0.832
Gnomad4 FIN exome
AF:
0.826
Gnomad4 NFE exome
AF:
0.872
Gnomad4 OTH exome
AF:
0.839
GnomAD4 genome
AF:
0.791
AC:
120452
AN:
152214
Hom.:
48650
Cov.:
35
AF XY:
0.790
AC XY:
58807
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.637
Gnomad4 AMR
AF:
0.864
Gnomad4 ASJ
AF:
0.880
Gnomad4 EAS
AF:
0.533
Gnomad4 SAS
AF:
0.839
Gnomad4 FIN
AF:
0.825
Gnomad4 NFE
AF:
0.873
Gnomad4 OTH
AF:
0.828
Alfa
AF:
0.854
Hom.:
81159
Bravo
AF:
0.786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
-0.060
CADD
Benign
13

Splicing

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: rs2856111; hg19: chr11-1075747; API