Variant rs2735727 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002458.3(MUC5B):c.2881-157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 636,530 control chromosomes in the GnomAD database, including 66,106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 14458 hom., cov: 33)

Exomes 𝑓: 0.45 ( 51648 hom. )

Consequence

MUC5B
NM_002458.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.48

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 (HGNC:):

MUC5B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 11-1236229-G-A is Benign according to our data. Variant chr11-1236229-G-A is described in ClinVar as [Benign]. Clinvar id is 1289456.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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.2881-157G>A		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.2881-157G>A		intron_variant		5	NM_002458.3	ENSP00000436812.1		Q9HC84
MUC5B	ENST00000525715.5 linkuse as main transcript	n.2939-157G>A		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64897

AN:

151904

Hom.:

14442

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.536

Gnomad AMR

AF:

0.538

Gnomad ASJ

AF:

0.442

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.433

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.438

Gnomad OTH

AF:

0.443

GnomAD4 exome

AF:

0.454

AC:

219954

AN:

484508

Hom.:

51648

AF XY:

0.452

AC XY:

112674

AN XY:

249306

show subpopulations

Gnomad4 AFR exome

AF:

0.306

Gnomad4 AMR exome

AF:

0.552

Gnomad4 ASJ exome

AF:

0.429

Gnomad4 EAS exome

AF:

0.710

Gnomad4 SAS exome

AF:

0.417

Gnomad4 FIN exome

AF:

0.494

Gnomad4 NFE exome

AF:

0.435

Gnomad4 OTH exome

AF:

0.446

GnomAD4 genome

AF:

0.427

AC:

64939

AN:

152022

Hom.:

14458

Cov.:

AF XY:

0.435

AC XY:

32338

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.314

Gnomad4 AMR

AF:

0.538

Gnomad4 ASJ

AF:

0.442

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.433

Gnomad4 FIN

AF:

0.511

Gnomad4 NFE

AF:

0.438

Gnomad4 OTH

AF:

0.448

Alfa

AF:

0.428

Hom.:

10764

Bravo

AF:

0.426

Asia WGS

AF:

0.568

AC:

1972

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

-0.99

CADD

Benign

0.19

DANN

Benign

0.66

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