Variant chr11-1083094-C-T details in Genebe, Genetics Data Aggregator

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

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]

MUC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

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

Synonymous conserved (PhyloP=-1.43 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC2	NM_002457.5 linkuse as main transcript	c.1386C>T	p.Ser462=	synonymous_variant	11/58	ENST00000713550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC2	ENST00000675028.1 linkuse as main transcript	c.1386C>T	p.Ser462=	synonymous_variant	11/30			P3
MUC2	ENST00000361558.7 linkuse as main transcript	n.1413C>T		non_coding_transcript_exon_variant	11/49	5

Frequencies

GnomAD3 genomes

AF:

0.00819

AC:

1246

AN:

152212

Hom.:

Cov.:

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.:

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.:

Cov.:

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

AF:

0.00821

AC:

1250

AN:

152330

Hom.:

Cov.:

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.:

Bravo

AF:

0.00640

Asia WGS

AF:

0.00866

AC:

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

MUC2: 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over