Variant 11-1078394-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_002457.5(MUC2):c.746C>T(p.Ala249Val) variant causes a missense change. The variant allele was found at a frequency of 0.00802 in 1,558,268 control chromosomes in the GnomAD database, including 57 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 1 hom., cov: 34)

Exomes 𝑓: 0.0083 ( 56 hom. )

Consequence

MUC2
NM_002457.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.88

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 11-1078394-C-T is Benign according to our data. Variant chr11-1078394-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2641117.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC2	NM_002457.5 linkuse as main transcript	c.746C>T	p.Ala249Val	missense_variant	6/58	ENST00000713550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC2	ENST00000675028.1 linkuse as main transcript	c.746C>T	p.Ala249Val	missense_variant	6/30			P3
MUC2	ENST00000361558.7 linkuse as main transcript	n.773C>T		non_coding_transcript_exon_variant	6/49	5

Frequencies

GnomAD3 genomes

AF:

0.00516

AC:

786

AN:

152250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00615

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00883

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00511

AC:

803

AN:

157190

Hom.:

AF XY:

0.00519

AC XY:

449

AN XY:

86438

show subpopulations

Gnomad AFR exome

AF:

0.00122

Gnomad AMR exome

AF:

0.00273

Gnomad ASJ exome

AF:

0.00305

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00172

Gnomad FIN exome

AF:

0.00193

Gnomad NFE exome

AF:

0.00938

Gnomad OTH exome

AF:

0.00636

GnomAD4 exome

AF:

0.00833

AC:

11708

AN:

1405900

Hom.:

Cov.:

AF XY:

0.00817

AC XY:

5689

AN XY:

695984

show subpopulations

Gnomad4 AFR exome

AF:

0.00118

Gnomad4 AMR exome

AF:

0.00346

Gnomad4 ASJ exome

AF:

0.00347

Gnomad4 EAS exome

AF:

0.0000273

Gnomad4 SAS exome

AF:

0.00192

Gnomad4 FIN exome

AF:

0.00187

Gnomad4 NFE exome

AF:

0.00990

Gnomad4 OTH exome

AF:

0.00711

GnomAD4 genome

AF:

0.00515

AC:

785

AN:

152368

Hom.:

Cov.:

AF XY:

0.00438

AC XY:

326

AN XY:

74512

show subpopulations

Gnomad4 AFR

AF:

0.00144

Gnomad4 AMR

AF:

0.00608

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00160

Gnomad4 NFE

AF:

0.00883

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00785

Hom.:

Bravo

AF:

0.00537

Asia WGS

AF:

0.000577

AC:

AN:

3478

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

MUC2: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

0.070

Cadd

Benign

Dann

Uncertain

1.0

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.

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