11-1017495-ATGC-A

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

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: -0.226
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]

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
MUC6NM_005961.3 linkuse as main transcriptc.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
MUC6ENST00000421673.7 linkuse as main transcriptc.5303_5305del p.Ser1768del inframe_deletion 31/335 NM_005961.3 ENSP00000406861 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
464
AN:
63282
Hom.:
0
Cov.:
0
FAILED QC
Gnomad AFR
AF:
0.0275
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00319
Gnomad ASJ
AF:
0.00282
Gnomad EAS
AF:
0.00261
Gnomad SAS
AF:
0.00390
Gnomad FIN
AF:
0.000566
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00132
Gnomad OTH
AF:
0.00915
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00162
AC:
1846
AN:
1137744
Hom.:
0
AF XY:
0.00208
AC XY:
1148
AN XY:
550806
show subpopulations
Gnomad4 AFR exome
AF:
0.00436
Gnomad4 AMR exome
AF:
0.00988
Gnomad4 ASJ exome
AF:
0.0103
Gnomad4 EAS exome
AF:
0.0000391
Gnomad4 SAS exome
AF:
0.0103
Gnomad4 FIN exome
AF:
0.00374
Gnomad4 NFE exome
AF:
0.000770
Gnomad4 OTH exome
AF:
0.00148
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff
AF:
0.00734
AC:
465
AN:
63344
Hom.:
0
Cov.:
0
AF XY:
0.00701
AC XY:
224
AN XY:
31970
show subpopulations
Gnomad4 AFR
AF:
0.0274
Gnomad4 AMR
AF:
0.00318
Gnomad4 ASJ
AF:
0.00282
Gnomad4 EAS
AF:
0.00262
Gnomad4 SAS
AF:
0.00389
Gnomad4 FIN
AF:
0.000566
Gnomad4 NFE
AF:
0.00132
Gnomad4 OTH
AF:
0.00913
Alfa
AF:
0.0715
Hom.:
0

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 providedresearchArun Kumar Laboratory, Indian Institute of ScienceJun 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.

Other links and lift over

dbSNP: rs752315234; hg19: chr11-1017495; API