Genetic Variant MUC5B:p.Arg2200Arg (chr11-1243480-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_002458.3(MUC5B):c.6600A>G(p.Arg2200Arg) 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 Benign (★★).

Frequency

Genomes: 𝑓 0.057 ( 224 hom., cov: 19)

Exomes 𝑓: 0.17 ( 73565 hom. )

Failed GnomAD Quality Control

Consequence

MUC5B
NM_002458.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.20

Variant links:

Genes affected

MUC5B (HGNC:7516): (mucin 5B, oligomeric mucus/gel-forming) This gene encodes a member of the mucin family of proteins, which are highly glycosylated macromolecular components of mucus secretions. This family member is the major gel-forming mucin in mucus. It is a major contributor to the lubricating and viscoelastic properties of whole saliva, normal lung mucus and cervical mucus. This gene has been found to be up-regulated in some human diseases, including sinus mucosa of chronic rhinosinusitis (CRS), CRS with nasal polyposis, chronic obstructive pulmonary disease (COPD) and H. pylori-associated gastric disease, and it may be involved in the pathogenesis of these diseases. [provided by RefSeq, Jul 2010]

MUC5B links:

MUC5B-AS1 (HGNC:53936): (MUC5B antisense RNA 1)

MUC5B-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 11-1243480-A-G is Benign according to our data. Variant chr11-1243480-A-G is described in ClinVar as [Benign]. Clinvar id is 403138.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.2 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC5B	NM_002458.3 link	c.6600A>G	p.Arg2200Arg	synonymous_variant	Exon 31 of 49	ENST00000529681.5	NP_002449.2	Q9HC84
MUC5B-AS1	NR_157183.1 link	n.57-842T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC5B	ENST00000529681.5 link	c.6600A>G	p.Arg2200Arg	synonymous_variant	Exon 31 of 49	5	NM_002458.3	ENSP00000436812.1		Q9HC84
MUC5B-AS1	ENST00000532061.2 link	n.57-842T>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

5352

AN:

94504

Hom.:

221

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0411

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0727

Gnomad ASJ

AF:

0.0592

Gnomad EAS

AF:

0.131

Gnomad SAS

AF:

0.0465

Gnomad FIN

AF:

0.0709

Gnomad MID

AF:

0.0773

Gnomad NFE

AF:

0.0592

Gnomad OTH

AF:

0.0568

GnomAD3 exomes

AF:

0.110

AC:

20414

AN:

185632

Hom.:

7177

AF XY:

0.109

AC XY:

10981

AN XY:

101016

show subpopulations

Gnomad AFR exome

AF:

0.0648

Gnomad AMR exome

AF:

0.108

Gnomad ASJ exome

AF:

0.0864

Gnomad EAS exome

AF:

0.390

Gnomad SAS exome

AF:

0.0955

Gnomad FIN exome

AF:

0.0597

Gnomad NFE exome

AF:

0.0976

Gnomad OTH exome

AF:

0.109

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.173

AC:

173019

AN:

999374

Hom.:

73565

Cov.:

104

AF XY:

0.171

AC XY:

84989

AN XY:

497640

show subpopulations

Gnomad4 AFR exome

AF:

0.0963

Gnomad4 AMR exome

AF:

0.187

Gnomad4 ASJ exome

AF:

0.157

Gnomad4 EAS exome

AF:

0.621

Gnomad4 SAS exome

AF:

0.140

Gnomad4 FIN exome

AF:

0.155

Gnomad4 NFE exome

AF:

0.166

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0568

AC:

5372

AN:

94604

Hom.:

224

Cov.:

AF XY:

0.0589

AC XY:

2707

AN XY:

45944

show subpopulations

Gnomad4 AFR

AF:

0.0413

Gnomad4 AMR

AF:

0.0728

Gnomad4 ASJ

AF:

0.0592

Gnomad4 EAS

AF:

0.131

Gnomad4 SAS

AF:

0.0468

Gnomad4 FIN

AF:

0.0709

Gnomad4 NFE

AF:

0.0592

Gnomad4 OTH

AF:

0.0642

Alfa

AF:

0.180

Hom.:

1107

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 09, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.6

DANN

Benign

0.59

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

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