Variant chr11-1017040-GGT-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1

The NM_005961.3(MUC6):c.5759_5760del(p.Tyr1920SerfsTer9) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.23 ( 0 hom., cov: 0)

Exomes 𝑓: 0.23 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MUC6
NM_005961.3 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:2

Conservation

PhyloP100: -0.539

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC6	NM_005961.3 linkuse as main transcript	c.5759_5760del	p.Tyr1920SerfsTer9	frameshift_variant	31/33	ENST00000421673.7	NP_005952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC6	ENST00000421673.7 linkuse as main transcript	c.5759_5760del	p.Tyr1920SerfsTer9	frameshift_variant	31/33	5	NM_005961.3	ENSP00000406861	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

32205

AN:

137794

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.320

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.255

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.241

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.232

AC:

186729

AN:

806088

Hom.:

AF XY:

0.243

AC XY:

99590

AN XY:

409538

show subpopulations

Gnomad4 AFR exome

AF:

0.280

Gnomad4 AMR exome

AF:

0.207

Gnomad4 ASJ exome

AF:

0.320

Gnomad4 EAS exome

AF:

0.364

Gnomad4 SAS exome

AF:

0.364

Gnomad4 FIN exome

AF:

0.267

Gnomad4 NFE exome

AF:

0.204

Gnomad4 OTH exome

AF:

0.249

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.234

AC:

32221

AN:

137902

Hom.:

Cov.:

AF XY:

0.234

AC XY:

15799

AN XY:

67426

show subpopulations

Gnomad4 AFR

AF:

0.264

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.258

Gnomad4 EAS

AF:

0.320

Gnomad4 SAS

AF:

0.322

Gnomad4 FIN

AF:

0.197

Gnomad4 NFE

AF:

0.223

Gnomad4 OTH

AF:

0.237

Alfa

AF:

0.331

Hom.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Small cell lung carcinoma

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

Lung cancer

Pathogenic:1

Pathogenic, no assertion criteria provided

research

Arun Kumar Laboratory, Indian Institute of Science

Jun 15, 2021

- -

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