11-1017495-ATGC-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM4_Supporting
The NM_005961.3(MUC6):c.5303_5305del(p.Ser1768del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0073 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0016 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MUC6
NM_005961.3 inframe_deletion
NM_005961.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.226
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_005961.3. Strenght limited to Supporting due to length of the change: 1aa.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUC6 | NM_005961.3 | c.5303_5305del | p.Ser1768del | inframe_deletion | 31/33 | ENST00000421673.7 | NP_005952.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUC6 | ENST00000421673.7 | c.5303_5305del | p.Ser1768del | inframe_deletion | 31/33 | 5 | NM_005961.3 | ENSP00000406861 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 464AN: 63282Hom.: 0 Cov.: 0 FAILED QC
GnomAD3 genomes
AF:
AC:
464
AN:
63282
Hom.:
Cov.:
0
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00162 AC: 1846AN: 1137744Hom.: 0 AF XY: 0.00208 AC XY: 1148AN XY: 550806
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1846
AN:
1137744
Hom.:
AF XY:
AC XY:
1148
AN XY:
550806
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.00734 AC: 465AN: 63344Hom.: 0 Cov.: 0 AF XY: 0.00701 AC XY: 224AN XY: 31970
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
AF:
AC:
465
AN:
63344
Hom.:
Cov.:
0
AF XY:
AC XY:
224
AN XY:
31970
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Lung cancer Pathogenic:1
Pathogenic, no assertion criteria provided | research | Arun Kumar Laboratory, Indian Institute of Science | Jun 15, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at