Variant chr11-1084609-G-A 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.1854G>A(p.Thr618=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 1,612,466 control chromosomes in the GnomAD database, including 5,466 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 0.059 ( 374 hom., cov: 35)

Exomes 𝑓: 0.079 ( 5092 hom. )

Consequence

MUC2
NM_002457.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP7

Synonymous conserved (PhyloP=-1.61 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0854 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.1854G>A	p.Thr618=	synonymous_variant	15/58	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.1854G>A	p.Thr618=	synonymous_variant	15/30			ENSP00000502432	P3
MUC2	ENST00000361558.7 linkuse as main transcript	n.1881G>A		non_coding_transcript_exon_variant	15/49	5

Frequencies

GnomAD3 genomes

AF:

0.0591

AC:

8989

AN:

152206

Hom.:

375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0152

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.0637

Gnomad ASJ

AF:

0.0806

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0304

Gnomad FIN

AF:

0.0754

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0872

Gnomad OTH

AF:

0.0603

GnomAD3 exomes

AF:

0.0621

AC:

15369

AN:

247600

Hom.:

617

AF XY:

0.0628

AC XY:

8467

AN XY:

134876

show subpopulations

Gnomad AFR exome

AF:

0.0130

Gnomad AMR exome

AF:

0.0449

Gnomad ASJ exome

AF:

0.0835

Gnomad EAS exome

AF:

0.000223

Gnomad SAS exome

AF:

0.0349

Gnomad FIN exome

AF:

0.0726

Gnomad NFE exome

AF:

0.0869

Gnomad OTH exome

AF:

0.0731

GnomAD4 exome

AF:

0.0791

AC:

115506

AN:

1460142

Hom.:

5092

Cov.:

AF XY:

0.0781

AC XY:

56752

AN XY:

726350

show subpopulations

Gnomad4 AFR exome

AF:

0.0132

Gnomad4 AMR exome

AF:

0.0466

Gnomad4 ASJ exome

AF:

0.0819

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0356

Gnomad4 FIN exome

AF:

0.0682

Gnomad4 NFE exome

AF:

0.0896

Gnomad4 OTH exome

AF:

0.0719

GnomAD4 genome

AF:

0.0590

AC:

8980

AN:

152324

Hom.:

374

Cov.:

AF XY:

0.0572

AC XY:

4260

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.0151

Gnomad4 AMR

AF:

0.0637

Gnomad4 ASJ

AF:

0.0806

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0299

Gnomad4 FIN

AF:

0.0754

Gnomad4 NFE

AF:

0.0872

Gnomad4 OTH

AF:

0.0597

Alfa

AF:

0.0756

Hom.:

279

Bravo

AF:

0.0572

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.0839

EpiControl

AF:

0.0871

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.11

DANN

Benign

0.86

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