Variant 11-1086366-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002457.5(MUC2):c.2494G>A(p.Gly832Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0823 in 1,613,088 control chromosomes in the GnomAD database, including 5,881 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.070 ( 413 hom., cov: 33)

Exomes 𝑓: 0.084 ( 5468 hom. )

Consequence

MUC2
NM_002457.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.59

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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 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.2494G>A	p.Gly832Ser	missense_variant	19/58	ENST00000713550.1	NP_002448.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC2	ENST00000675028.1 linkuse as main transcript	c.2494G>A	p.Gly832Ser	missense_variant	19/30			ENSP00000502432	P3
MUC2	ENST00000361558.7 linkuse as main transcript	n.2521G>A		non_coding_transcript_exon_variant	19/49	5

Frequencies

GnomAD3 genomes

AF:

0.0696

AC:

10593

AN:

152124

Hom.:

413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0396

Gnomad AMI

AF:

0.0452

Gnomad AMR

AF:

0.0517

Gnomad ASJ

AF:

0.0404

Gnomad EAS

AF:

0.0603

Gnomad SAS

AF:

0.0478

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0897

Gnomad OTH

AF:

0.0664

GnomAD3 exomes

AF:

0.0706

AC:

17500

AN:

247974

Hom.:

706

AF XY:

0.0710

AC XY:

9578

AN XY:

134982

show subpopulations

Gnomad AFR exome

AF:

0.0403

Gnomad AMR exome

AF:

0.0358

Gnomad ASJ exome

AF:

0.0454

Gnomad EAS exome

AF:

0.0641

Gnomad SAS exome

AF:

0.0517

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0856

Gnomad OTH exome

AF:

0.0722

GnomAD4 exome

AF:

0.0836

AC:

122186

AN:

1460846

Hom.:

5468

Cov.:

AF XY:

0.0828

AC XY:

60154

AN XY:

726688

show subpopulations

Gnomad4 AFR exome

AF:

0.0413

Gnomad4 AMR exome

AF:

0.0382

Gnomad4 ASJ exome

AF:

0.0448

Gnomad4 EAS exome

AF:

0.0449

Gnomad4 SAS exome

AF:

0.0522

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.0906

Gnomad4 OTH exome

AF:

0.0788

GnomAD4 genome

AF:

0.0696

AC:

10596

AN:

152242

Hom.:

413

Cov.:

AF XY:

0.0695

AC XY:

5173

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0396

Gnomad4 AMR

AF:

0.0516

Gnomad4 ASJ

AF:

0.0404

Gnomad4 EAS

AF:

0.0605

Gnomad4 SAS

AF:

0.0472

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.0897

Gnomad4 OTH

AF:

0.0658

Alfa

AF:

0.0797

Hom.:

1069

Bravo

AF:

0.0640

Asia WGS

AF:

0.0600

AC:

208

AN:

3478

EpiCase

AF:

0.0857

EpiControl

AF:

0.0804

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

0.040

CADD

Uncertain

DANN

Uncertain

0.99

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.66

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.66

Position offset: 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