chr11-1016890-G-A

Position:

• chr11-1016890-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_005961.3(MUC6):​c.5911C>T​(p.Pro1971Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.48 (1 hom., cov: 187)
  • Exomes 𝑓: 0.47 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC6 NM_005961.3 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -5.41

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0014880002).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC6	NM_005961.3	c.5911C>T	p.Pro1971Ser	missense_variant	31/33	ENST00000421673.7	NP_005952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC6	ENST00000421673.7	c.5911C>T	p.Pro1971Ser	missense_variant	31/33	5	NM_005961.3	ENSP00000406861	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 50632 AN: 105982 Hom.: 1 Cov.: 187 FAILED QC

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.470

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.472 AC: 463690 AN: 981546 Hom.: 0 Cov.: 461 AF XY: 0.474 AC XY: 235911 AN XY: 497896

Gnomad4 AFR exome AF: 0.491

Gnomad4 AMR exome AF: 0.485

Gnomad4 ASJ exome AF: 0.483

Gnomad4 EAS exome AF: 0.489

Gnomad4 SAS exome AF: 0.481

Gnomad4 FIN exome AF: 0.470

Gnomad4 NFE exome AF: 0.469

Gnomad4 OTH exome AF: 0.476

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.478 AC: 50666 AN: 106054 Hom.: 1 Cov.: 187 AF XY: 0.477 AC XY: 24979 AN XY: 52348

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.469

Alfa AF: 0.445 Hom.: 0

ExAC AF: 0.199 AC: 24136

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

literature only

James Howe Lab, University of Iowa Hospital and Clinics

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.069
BayesDel_addAF	Benign	-0.39	T
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Uncertain	0.98
DEOGEN2	Benign	0.032	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.0094	N
MetaRNN	Benign	0.0015	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	1.8	L
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.17	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.11
Sift	Benign	0.13	T
Sift4G	Benign	0.17	T
Polyphen		0.0030	B
Vest4		0.024
MPC		0.43
ClinPred		0.011	T
GERP RS		-6.2
Varity_R		0.023
gMVP		0.10

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

Other links and lift over

dbSNP: rs113508205; hg19: chr11-1016890; COSMIC: COSV70132142; COSMIC: COSV70132142;