rs201236828

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002458.3(MUC5B):c.9140C>A(p.Thr3047Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 1,590,254 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 0 hom., cov: 29)

Exomes 𝑓: 0.022 ( 0 hom. )

Consequence

MUC5B
NM_002458.3 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.239

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0032743812).

BP6

Variant 11-1246020-C-A is Benign according to our data. Variant chr11-1246020-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 403186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0194 (2923/150452) while in subpopulation NFE AF= 0.0278 (1868/67290). AF 95% confidence interval is 0.0267. There are 0 homozygotes in gnomad4. There are 1445 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2923 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC5B	NM_002458.3 link	c.9140C>A	p.Thr3047Asn	missense_variant	Exon 31 of 49	ENST00000529681.5	NP_002449.2	Q9HC84
MUC5B-AS1	NR_157183.1 link	n.57-3382G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC5B	ENST00000529681.5 link	c.9140C>A	p.Thr3047Asn	missense_variant	Exon 31 of 49	5	NM_002458.3	ENSP00000436812.1		Q9HC84
MUC5B-AS1	ENST00000532061.2 link	n.57-3382G>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.0194

AC:

2923

AN:

150334

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00539

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00547

Gnomad ASJ

AF:

0.0250

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.00648

Gnomad FIN

AF:

0.0579

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0278

Gnomad OTH

AF:

0.0155

GnomAD3 exomes

AF:

0.0224

AC:

5542

AN:

247340

Hom.:

AF XY:

0.0222

AC XY:

2973

AN XY:

134206

show subpopulations

Gnomad AFR exome

AF:

0.00554

Gnomad AMR exome

AF:

0.00432

Gnomad ASJ exome

AF:

0.0227

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00745

Gnomad FIN exome

AF:

0.0658

Gnomad NFE exome

AF:

0.0296

Gnomad OTH exome

AF:

0.0245

GnomAD4 exome

AF:

0.0222

AC:

31999

AN:

1439802

Hom.:

Cov.:

AF XY:

0.0220

AC XY:

15786

AN XY:

716818

show subpopulations

Gnomad4 AFR exome

AF:

0.00307

Gnomad4 AMR exome

AF:

0.00435

Gnomad4 ASJ exome

AF:

0.0233

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00751

Gnomad4 FIN exome

AF:

0.0651

Gnomad4 NFE exome

AF:

0.0236

Gnomad4 OTH exome

AF:

0.0211

GnomAD4 genome

AF:

0.0194

AC:

2923

AN:

150452

Hom.:

Cov.:

AF XY:

0.0197

AC XY:

1445

AN XY:

73482

show subpopulations

Gnomad4 AFR

AF:

0.00537

Gnomad4 AMR

AF:

0.00546

Gnomad4 ASJ

AF:

0.0250

Gnomad4 EAS

AF:

0.000196

Gnomad4 SAS

AF:

0.00649

Gnomad4 FIN

AF:

0.0579

Gnomad4 NFE

AF:

0.0278

Gnomad4 OTH

AF:

0.0153

Alfa

AF:

0.0246

Hom.:

ESP6500AA

AF:

0.00428

AC:

ESP6500EA

AF:

0.0199

AC:

167

ExAC

AF:

0.0267

AC:

3238

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely 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 -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.63

DEOGEN2

Benign

0.022

Eigen

Benign

-0.17

Eigen_PC

Benign

-0.40

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.39

MetaRNN

Benign

0.0033

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.3

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.98

REVEL

Benign

0.10

Sift

Benign

0.12

Vest4

0.045

ClinPred

0.012

GERP RS

2.8

Varity_R

0.054

gMVP

0.22

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