Variant chr11-1240410-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002458.3(MUC5B):c.3970+35C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 1,540,660 control chromosomes in the GnomAD database, including 161,191 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 14868 hom., cov: 33)

Exomes 𝑓: 0.46 ( 146323 hom. )

Consequence

MUC5B
NM_002458.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.57

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 11-1240410-C-T is Benign according to our data. Variant chr11-1240410-C-T is described in ClinVar as [Benign]. Clinvar id is 1251061.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 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.3970+35C>T		intron_variant		ENST00000529681.5	NP_002449.2	Q9HC84

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC5B	ENST00000529681.5 linkuse as main transcript	c.3970+35C>T		intron_variant		5	NM_002458.3	ENSP00000436812.1		Q9HC84

Frequencies

GnomAD3 genomes

AF:

0.433

AC:

65742

AN:

151860

Hom.:

14848

Cov.:

show subpopulations

Gnomad AFR

AF:

0.317

Gnomad AMI

AF:

0.537

Gnomad AMR

AF:

0.538

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.661

Gnomad SAS

AF:

0.439

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.445

GnomAD3 exomes

AF:

0.486

AC:

99953

AN:

205676

Hom.:

25069

AF XY:

0.481

AC XY:

52977

AN XY:

110044

show subpopulations

Gnomad AFR exome

AF:

0.306

Gnomad AMR exome

AF:

0.602

Gnomad ASJ exome

AF:

0.447

Gnomad EAS exome

AF:

0.663

Gnomad SAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.510

Gnomad NFE exome

AF:

0.456

Gnomad OTH exome

AF:

0.474

GnomAD4 exome

AF:

0.455

AC:

632526

AN:

1388682

Hom.:

146323

Cov.:

AF XY:

0.454

AC XY:

310384

AN XY:

683114

show subpopulations

Gnomad4 AFR exome

AF:

0.307

Gnomad4 AMR exome

AF:

0.589

Gnomad4 ASJ exome

AF:

0.432

Gnomad4 EAS exome

AF:

0.697

Gnomad4 SAS exome

AF:

0.432

Gnomad4 FIN exome

AF:

0.504

Gnomad4 NFE exome

AF:

0.447

Gnomad4 OTH exome

AF:

0.449

GnomAD4 genome

AF:

0.433

AC:

65790

AN:

151978

Hom.:

14868

Cov.:

AF XY:

0.441

AC XY:

32745

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.317

Gnomad4 AMR

AF:

0.539

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.661

Gnomad4 SAS

AF:

0.439

Gnomad4 FIN

AF:

0.523

Gnomad4 NFE

AF:

0.446

Gnomad4 OTH

AF:

0.450

Alfa

AF:

0.422

Hom.:

3408

Bravo

AF:

0.431

Asia WGS

AF:

0.577

AC:

2004

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.23

DANN

Benign

0.33

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