chr11-1018400-G-A

Position:

• chr11-1018400-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_005961.3(MUC6):​c.4401C>T​(p.His1467=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00022 (0 hom., cov: 57)
  • Exomes 𝑓: 0.000015 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC6 NM_005961.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.02

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 Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 11-1018400-G-A is Benign according to our data. Variant chr11-1018400-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2641109.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-3.02 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC6	NM_005961.3	c.4401C>T	p.His1467=	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	c.4401C>T	p.His1467=	synonymous_variant	31/33	5	NM_005961.3	ENSP00000406861	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 29 AN: 130660 Hom.: 0 Cov.: 57 FAILED QC

Gnomad AFR AF: 0.000351

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000230

Gnomad ASJ AF: 0.000324

Gnomad EAS AF: 0.000223

Gnomad SAS AF: 0.000724

Gnomad FIN AF: 0.000323

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000101

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000150 AC: 21 AN: 1401352 Hom.: 0 Cov.: 207 AF XY: 0.0000100 AC XY: 7 AN XY: 697866

Gnomad4 AFR exome AF: 0.0000313

Gnomad4 AMR exome AF: 0.0000235

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000154

Gnomad4 SAS exome AF: 0.0000239

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000753

Gnomad4 OTH exome AF: 0.0000343

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000222 AC: 29 AN: 130734 Hom.: 0 Cov.: 57 AF XY: 0.000252 AC XY: 16 AN XY: 63454

Gnomad4 AFR AF: 0.000350

Gnomad4 AMR AF: 0.000230

Gnomad4 ASJ AF: 0.000324

Gnomad4 EAS AF: 0.000224

Gnomad4 SAS AF: 0.000724

Gnomad4 FIN AF: 0.000323

Gnomad4 NFE AF: 0.000101

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00386 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	-0.92
CADD	Benign	1.3
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs748438008; hg19: chr11-1018400;