Variant 11-1247452-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002458.3(MUC5B):c.10572T>C(p.Ser3524Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,604,788 control chromosomes in the GnomAD database, including 28,568 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2386 hom., cov: 27)

Exomes 𝑓: 0.17 ( 26182 hom. )

Consequence

MUC5B
NM_002458.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.14

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:):

MUC5B-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 11-1247452-T-C is Benign according to our data. Variant chr11-1247452-T-C is described in ClinVar as [Benign]. Clinvar id is 403164.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-4.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC5B	NM_002458.3 linkuse as main transcript	c.10572T>C	p.Ser3524Ser	synonymous_variant	31/49	ENST00000529681.5	NP_002449.2	Q9HC84
MUC5B-AS1	NR_157183.1 linkuse as main transcript	n.56+2169A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC5B	ENST00000529681.5 linkuse as main transcript	c.10572T>C	p.Ser3524Ser	synonymous_variant	31/49	5	NM_002458.3	ENSP00000436812.1		Q9HC84
MUC5B-AS1	ENST00000532061.2 linkuse as main transcript	n.56+2169A>G		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

24283

AN:

147254

Hom.:

2385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.180

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.00517

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.163

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.154

GnomAD3 exomes

AF:

0.152

AC:

37502

AN:

247502

Hom.:

4388

AF XY:

0.156

AC XY:

21021

AN XY:

134458

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.0830

Gnomad ASJ exome

AF:

0.156

Gnomad EAS exome

AF:

0.00345

Gnomad SAS exome

AF:

0.150

Gnomad FIN exome

AF:

0.217

Gnomad NFE exome

AF:

0.183

Gnomad OTH exome

AF:

0.157

GnomAD4 exome

AF:

0.174

AC:

254180

AN:

1457416

Hom.:

26182

Cov.:

133

AF XY:

0.174

AC XY:

126298

AN XY:

725092

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.0871

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.00214

Gnomad4 SAS exome

AF:

0.149

Gnomad4 FIN exome

AF:

0.205

Gnomad4 NFE exome

AF:

0.186

Gnomad4 OTH exome

AF:

0.170

GnomAD4 genome

AF:

0.165

AC:

24294

AN:

147372

Hom.:

2386

Cov.:

AF XY:

0.163

AC XY:

11724

AN XY:

71786

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.125

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.00518

Gnomad4 SAS

AF:

0.139

Gnomad4 FIN

AF:

0.216

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.155

Alfa

AF:

0.174

Hom.:

1259

Bravo

AF:

0.155

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

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

-0.95

CADD

Benign

3.7

DANN

Benign

0.84

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