11-1247407-G-T

Variant names:

Variant summary

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

The NM_002458.3(MUC5B):c.10527G>T(p.Leu3509Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,562,312 control chromosomes in the GnomAD database, including 16,776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1613 hom., cov: 26)

Exomes 𝑓: 0.13 ( 15163 hom. )

Consequence

MUC5B
NM_002458.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.00600

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 -21 ACMG points.

BP4

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

BP6

Variant 11-1247407-G-T is Benign according to our data. Variant chr11-1247407-G-T is described in ClinVar as [Benign]. Clinvar id is 403163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.006 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC5B	NM_002458.3 link	c.10527G>T	p.Leu3509Leu	synonymous_variant	Exon 31 of 49	ENST00000529681.5	NP_002449.2	Q9HC84
MUC5B-AS1	NR_157183.1 link	n.56+2214C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC5B	ENST00000529681.5 link	c.10527G>T	p.Leu3509Leu	synonymous_variant	Exon 31 of 49	5	NM_002458.3	ENSP00000436812.1		Q9HC84
MUC5B-AS1	ENST00000532061.2 link	n.56+2214C>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

19926

AN:

134526

Hom.:

1613

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.0691

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.144

GnomAD3 exomes

AF:

0.153

AC:

36218

AN:

237222

Hom.:

3967

AF XY:

0.148

AC XY:

19085

AN XY:

129210

show subpopulations

Gnomad AFR exome

AF:

0.0926

Gnomad AMR exome

AF:

0.284

Gnomad ASJ exome

AF:

0.133

Gnomad EAS exome

AF:

0.0521

Gnomad SAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.229

Gnomad NFE exome

AF:

0.128

Gnomad OTH exome

AF:

0.152

GnomAD4 exome

AF:

0.133

AC:

190203

AN:

1427686

Hom.:

15163

Cov.:

117

AF XY:

0.134

AC XY:

94993

AN XY:

710692

show subpopulations

Gnomad4 AFR exome

AF:

0.0928

Gnomad4 AMR exome

AF:

0.275

Gnomad4 ASJ exome

AF:

0.132

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.222

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.148

AC:

19931

AN:

134626

Hom.:

1613

Cov.:

AF XY:

0.156

AC XY:

10201

AN XY:

65486

show subpopulations

Gnomad4 AFR

AF:

0.108

Gnomad4 AMR

AF:

0.228

Gnomad4 ASJ

AF:

0.150

Gnomad4 EAS

AF:

0.0693

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.143

Gnomad4 OTH

AF:

0.143

Alfa

AF:

0.0970

Hom.:

213

Bravo

AF:

0.135

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 09, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: 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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.2

DANN

Benign

0.56

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