Variant chr11-1107741-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002457.5(MUC2):c.11682T>C(p.Pro3894Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 1,612,670 control chromosomes in the GnomAD database, including 240,236 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 24937 hom., cov: 33)

Exomes 𝑓: 0.53 ( 215299 hom. )

Consequence

MUC2
NM_002457.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.47

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]

MUC2 links:

MUC2 (HGNC:):

MUC2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP7

Synonymous conserved (PhyloP=-2.47 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC2	NM_002457.5 linkuse as main transcript	c.11682T>C	p.Pro3894Pro	synonymous_variant	51/58		NP_002448.5	Q02817A0A3S8TMF2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC2	ENST00000674892.1 linkuse as main transcript	c.2166T>C	p.Pro722Pro	synonymous_variant	13/20			ENSP00000501871.1		A0A6Q8PFN2
MUC2	ENST00000361558.7 linkuse as main transcript	n.11719T>C		non_coding_transcript_exon_variant	42/49	5

Frequencies

GnomAD3 genomes

AF:

0.563

AC:

85653

AN:

152012

Hom.:

24896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.575

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.993

Gnomad SAS

AF:

0.636

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.507

Gnomad OTH

AF:

0.545

GnomAD3 exomes

AF:

0.584

AC:

144845

AN:

248048

Hom.:

44655

AF XY:

0.577

AC XY:

77862

AN XY:

135036

show subpopulations

Gnomad AFR exome

AF:

0.624

Gnomad AMR exome

AF:

0.653

Gnomad ASJ exome

AF:

0.412

Gnomad EAS exome

AF:

0.994

Gnomad SAS exome

AF:

0.621

Gnomad FIN exome

AF:

0.553

Gnomad NFE exome

AF:

0.504

Gnomad OTH exome

AF:

0.551

GnomAD4 exome

AF:

0.534

AC:

779752

AN:

1460538

Hom.:

215299

Cov.:

AF XY:

0.535

AC XY:

388420

AN XY:

726550

show subpopulations

Gnomad4 AFR exome

AF:

0.626

Gnomad4 AMR exome

AF:

0.645

Gnomad4 ASJ exome

AF:

0.412

Gnomad4 EAS exome

AF:

0.994

Gnomad4 SAS exome

AF:

0.617

Gnomad4 FIN exome

AF:

0.563

Gnomad4 NFE exome

AF:

0.505

Gnomad4 OTH exome

AF:

0.547

GnomAD4 genome

AF:

0.564

AC:

85757

AN:

152132

Hom.:

24937

Cov.:

AF XY:

0.568

AC XY:

42248

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.620

Gnomad4 AMR

AF:

0.576

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.993

Gnomad4 SAS

AF:

0.636

Gnomad4 FIN

AF:

0.534

Gnomad4 NFE

AF:

0.507

Gnomad4 OTH

AF:

0.550

Alfa

AF:

0.515

Hom.:

35005

Bravo

AF:

0.571

Asia WGS

AF:

0.833

AC:

2897

AN:

3478

EpiCase

AF:

0.494

EpiControl

AF:

0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.12

DANN

Benign

0.34

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over