Variant chr11-1233859-CCCCTG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002458.3(MUC5B):c.2377+30_2377+34del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 1,567,680 control chromosomes in the GnomAD database, including 154,485 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.42 ( 14045 hom., cov: 0)

Exomes 𝑓: 0.44 ( 140440 hom. )

Consequence

MUC5B
NM_002458.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.02

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 -10 ACMG points.

BP6

Variant 11-1233859-CCCCTG-C is Benign according to our data. Variant chr11-1233859-CCCCTG-C is described in ClinVar as [Benign]. Clinvar id is 403127.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC5B	NM_002458.3 linkuse as main transcript	c.2377+30_2377+34del		intron_variant		ENST00000529681.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC5B	ENST00000529681.5 linkuse as main transcript	c.2377+30_2377+34del		intron_variant		5	NM_002458.3	P1
MUC5B	ENST00000525715.5 linkuse as main transcript	n.2435+30_2435+34del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.422

AC:

63675

AN:

150886

Hom.:

14027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.531

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.653

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.505

Gnomad MID

AF:

0.398

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.437

GnomAD3 exomes

AF:

0.442

AC:

80149

AN:

181460

Hom.:

19525

AF XY:

0.434

AC XY:

42426

AN XY:

97810

show subpopulations

Gnomad AFR exome

AF:

0.254

Gnomad AMR exome

AF:

0.571

Gnomad ASJ exome

AF:

0.419

Gnomad EAS exome

AF:

0.641

Gnomad SAS exome

AF:

0.404

Gnomad FIN exome

AF:

0.469

Gnomad NFE exome

AF:

0.398

Gnomad OTH exome

AF:

0.445

GnomAD4 exome

AF:

0.438

AC:

620414

AN:

1416678

Hom.:

140440

AF XY:

0.437

AC XY:

306345

AN XY:

701694

show subpopulations

Gnomad4 AFR exome

AF:

0.289

Gnomad4 AMR exome

AF:

0.561

Gnomad4 ASJ exome

AF:

0.423

Gnomad4 EAS exome

AF:

0.693

Gnomad4 SAS exome

AF:

0.417

Gnomad4 FIN exome

AF:

0.483

Gnomad4 NFE exome

AF:

0.430

Gnomad4 OTH exome

AF:

0.435

GnomAD4 genome

AF:

0.422

AC:

63721

AN:

151002

Hom.:

14045

Cov.:

AF XY:

0.430

AC XY:

31707

AN XY:

73738

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.536

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.654

Gnomad4 SAS

AF:

0.430

Gnomad4 FIN

AF:

0.505

Gnomad4 NFE

AF:

0.436

Gnomad4 OTH

AF:

0.442

Asia WGS

AF:

0.561

AC:

1946

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

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

Splicing

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