Genetic Variant NM_005961.3:c.5760C>A (chr11-1017041-G-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005961.3(MUC6):c.5760C>A(p.Tyr1920*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.054 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000064 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MUC6
NM_005961.3 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.70

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 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC6	NM_005961.3 link	c.5760C>A	p.Tyr1920*	stop_gained	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.5760C>A	p.Tyr1920*	stop_gained	Exon 31 of 33	5	NM_005961.3	ENSP00000406861.2		Q6W4X9

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

504

AN:

9266

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0619

Gnomad AMI

AF:

0.0385

Gnomad AMR

AF:

0.0627

Gnomad ASJ

AF:

0.0625

Gnomad EAS

AF:

0.0645

Gnomad SAS

AF:

0.103

Gnomad FIN

AF:

0.0744

Gnomad MID

AF:

0.125

Gnomad NFE

AF:

0.0361

Gnomad OTH

AF:

0.0448

GnomAD4 exome

AF:

0.0000642

AC:

AN:

405042

Hom.:

Cov.:

AF XY:

0.0000870

AC XY:

AN XY:

195500

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000387

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000311

Gnomad4 FIN exome

AF:

0.00106

Gnomad4 NFE exome

AF:

0.0000151

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

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

AF:

0.0543

AC:

503

AN:

9260

Hom.:

Cov.:

AF XY:

0.0604

AC XY:

290

AN XY:

4798

show subpopulations

Gnomad4 AFR

AF:

0.0617

Gnomad4 AMR

AF:

0.0626

Gnomad4 ASJ

AF:

0.0625

Gnomad4 EAS

AF:

0.0645

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.0744

Gnomad4 NFE

AF:

0.0359

Gnomad4 OTH

AF:

0.0448

Alfa

AF:

0.473

Hom.:

ExAC

AF:

0.000181

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.24

BayesDel_noAF

Uncertain

0.11

CADD

Uncertain

DANN

Benign

0.89

Eigen

Benign

-0.71

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.0020

Vest4

0.069

GERP RS

-6.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over