11-1094482-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_002457.5(MUC2):c.4239G>A(p.Thr1413=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000017 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC2 NM_002457.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.73

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]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 11-1094482-G-A is Benign according to our data. Variant chr11-1094482-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2641127.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.73 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC2	NM_002457.5	c.4239G>A	p.Thr1413=	synonymous_variant	30/58	ENST00000713550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC2	ENST00000361558.7	n.4266G>A		non_coding_transcript_exon_variant	30/49	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 77 AN: 53572 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00235

Gnomad AMI AF: 0.00365

Gnomad AMR AF: 0.000661

Gnomad ASJ AF: 0.00229

Gnomad EAS AF: 0.00199

Gnomad SAS AF: 0.00416

Gnomad FIN AF: 0.00109

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000988

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000167 AC: 19 AN: 1135410 Hom.: 0 Cov.: 37 AF XY: 0.0000236 AC XY: 13 AN XY: 551270

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000533

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000277

Gnomad4 NFE exome AF: 0.0000174

Gnomad4 OTH exome AF: 0.0000239

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00144 AC: 77 AN: 53636 Hom.: 0 Cov.: 0 AF XY: 0.00153 AC XY: 41 AN XY: 26880

Gnomad4 AFR AF: 0.00234

Gnomad4 AMR AF: 0.000660

Gnomad4 ASJ AF: 0.00229

Gnomad4 EAS AF: 0.00200

Gnomad4 SAS AF: 0.00416

Gnomad4 FIN AF: 0.00109

Gnomad4 NFE AF: 0.000988

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000970 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

MUC2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.49
Dann	Benign	0.19

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs75494928; hg19: chr11-1092420;