Variant chr11-1017566-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_005961.3(MUC6):c.5235C>T(p.Thr1745=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,104,954 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00098 ( 0 hom., cov: 72)

Exomes 𝑓: 0.000033 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MUC6
NM_005961.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.241

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 Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 11-1017566-G-A is Benign according to our data. Variant chr11-1017566-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2641106.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.241 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC6	NM_005961.3 linkuse as main transcript	c.5235C>T	p.Thr1745=	synonymous_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.5235C>T	p.Thr1745=	synonymous_variant	31/33	5	NM_005961.3	ENSP00000406861	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

72764

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000837

Gnomad AMI

AF:

0.00718

Gnomad AMR

AF:

0.00245

Gnomad ASJ

AF:

0.000509

Gnomad EAS

AF:

0.000816

Gnomad SAS

AF:

0.000681

Gnomad FIN

AF:

0.00124

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000738

Gnomad OTH

AF:

0.00192

GnomAD3 exomes

AF:

0.00000410

AC:

AN:

244080

Hom.:

AF XY:

0.00

AC XY:

AN XY:

132558

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000908

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000335

AC:

AN:

1104954

Hom.:

Cov.:

244

AF XY:

0.0000439

AC XY:

AN XY:

547296

show subpopulations

Gnomad4 AFR exome

AF:

0.0000397

Gnomad4 AMR exome

AF:

0.0000995

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000830

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000586

Gnomad4 NFE exome

AF:

0.0000291

Gnomad4 OTH exome

AF:

0.0000454

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000976

AC:

AN:

72776

Hom.:

Cov.:

AF XY:

0.000837

AC XY:

AN XY:

35822

show subpopulations

Gnomad4 AFR

AF:

0.000835

Gnomad4 AMR

AF:

0.00229

Gnomad4 ASJ

AF:

0.000509

Gnomad4 EAS

AF:

0.000817

Gnomad4 SAS

AF:

0.000680

Gnomad4 FIN

AF:

0.00124

Gnomad4 NFE

AF:

0.000738

Gnomad4 OTH

AF:

0.00192

Alfa

AF:

0.0226

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Aug 01, 2023

MUC6: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.5

DANN

Benign

0.58

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