Variant chr11-1107170-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002457.5(MUC2):c.11497A>G(p.Ser3833Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 1,612,550 control chromosomes in the GnomAD database, including 4,681 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.087 ( 686 hom., cov: 33)

Exomes 𝑓: 0.072 ( 3995 hom. )

Consequence

MUC2
NM_002457.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91

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 Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC2	NM_002457.5 linkuse as main transcript	c.11497A>G	p.Ser3833Gly	missense_variant	50/58	ENST00000713550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC2	ENST00000674892.1 linkuse as main transcript	c.1981A>G	p.Ser661Gly	missense_variant	12/20			A2
MUC2	ENST00000361558.7 linkuse as main transcript	n.11534A>G		non_coding_transcript_exon_variant	41/49	5

Frequencies

GnomAD3 genomes

AF:

0.0870

AC:

13237

AN:

152218

Hom.:

685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.0578

Gnomad ASJ

AF:

0.0268

Gnomad EAS

AF:

0.0431

Gnomad SAS

AF:

0.0517

Gnomad FIN

AF:

0.0954

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0731

Gnomad OTH

AF:

0.0783

GnomAD3 exomes

AF:

0.0674

AC:

16715

AN:

247940

Hom.:

663

AF XY:

0.0658

AC XY:

8884

AN XY:

135034

show subpopulations

Gnomad AFR exome

AF:

0.144

Gnomad AMR exome

AF:

0.0370

Gnomad ASJ exome

AF:

0.0342

Gnomad EAS exome

AF:

0.0542

Gnomad SAS exome

AF:

0.0512

Gnomad FIN exome

AF:

0.0981

Gnomad NFE exome

AF:

0.0699

Gnomad OTH exome

AF:

0.0689

GnomAD4 exome

AF:

0.0716

AC:

104535

AN:

1460214

Hom.:

3995

Cov.:

AF XY:

0.0706

AC XY:

51294

AN XY:

726310

show subpopulations

Gnomad4 AFR exome

AF:

0.147

Gnomad4 AMR exome

AF:

0.0402

Gnomad4 ASJ exome

AF:

0.0335

Gnomad4 EAS exome

AF:

0.0376

Gnomad4 SAS exome

AF:

0.0508

Gnomad4 FIN exome

AF:

0.0993

Gnomad4 NFE exome

AF:

0.0731

Gnomad4 OTH exome

AF:

0.0722

GnomAD4 genome

AF:

0.0869

AC:

13241

AN:

152336

Hom.:

686

Cov.:

AF XY:

0.0856

AC XY:

6374

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.0578

Gnomad4 ASJ

AF:

0.0268

Gnomad4 EAS

AF:

0.0430

Gnomad4 SAS

AF:

0.0511

Gnomad4 FIN

AF:

0.0954

Gnomad4 NFE

AF:

0.0731

Gnomad4 OTH

AF:

0.0766

Alfa

AF:

0.0718

Hom.:

653

Bravo

AF:

0.0852

Asia WGS

AF:

0.0660

AC:

229

AN:

3478

EpiCase

AF:

0.0710

EpiControl

AF:

0.0685

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.14

DANN

Benign

0.30

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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