Variant NM_005961.3:c.4631_4633delCGA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PM4_SupportingBP6_Moderate

The NM_005961.3(MUC6):c.4631_4633delCGA(p.Thr1544del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00195 in 1,315,560 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0019 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MUC6
NM_005961.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0860

Variant links:

Genes affected

MUC6 (HGNC:7517): (mucin 6, oligomeric mucus/gel-forming) This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins produced by many epithelial tissues. The protein encoded by this gene is secreted and forms an insoluble mucous barrier that protects the gut lumen. [provided by RefSeq, Dec 2016]

MUC6 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Variant has high frequency in the AMR(1.2774E-4) population. However there is too low homozygotes in high coverage region: (expected more than 1, got 0).

PM4

Nonframeshift variant in NON repetitive region in NM_005961.3. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 11-1018167-ATCG-A is Benign according to our data. Variant chr11-1018167-ATCG-A is described in ClinVar as [Benign]. Clinvar id is 403202.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC6	NM_005961.3 link	c.4631_4633delCGA	p.Thr1544del	disruptive_inframe_deletion	Exon 31 of 33	ENST00000421673.7	NP_005952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC6	ENST00000421673.7 link	c.4631_4633delCGA	p.Thr1544del	disruptive_inframe_deletion	Exon 31 of 33	5	NM_005961.3	ENSP00000406861.2		Q6W4X9

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

105212

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000273

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000355

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000318

Gnomad SAS

AF:

0.000346

Gnomad FIN

AF:

0.000141

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000992

Gnomad OTH

AF:

0.000680

GnomAD4 exome

AF:

0.00195

AC:

2565

AN:

1315560

Hom.:

AF XY:

0.00233

AC XY:

1528

AN XY:

655462

show subpopulations

Gnomad4 AFR exome

AF:

0.00295

Gnomad4 AMR exome

AF:

0.0112

Gnomad4 ASJ exome

AF:

0.00792

Gnomad4 EAS exome

AF:

0.000262

Gnomad4 SAS exome

AF:

0.00977

Gnomad4 FIN exome

AF:

0.00222

Gnomad4 NFE exome

AF:

0.000891

Gnomad4 OTH exome

AF:

0.00181

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000190

AC:

AN:

105260

Hom.:

Cov.:

AF XY:

0.000254

AC XY:

AN XY:

51142

show subpopulations

Gnomad4 AFR

AF:

0.000273

Gnomad4 AMR

AF:

0.000354

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000319

Gnomad4 SAS

AF:

0.000348

Gnomad4 FIN

AF:

0.000141

Gnomad4 NFE

AF:

0.0000992

Gnomad4 OTH

AF:

0.000669

Alfa

AF:

0.0301

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 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

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