NM_005961.3:c.5667C>G

Variant names:

• chr11-1017134-G-C
• rs201950836
• NM_005961.3:c.5667C>G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_005961.3(MUC6):​c.5667C>G​(p.Thr1889Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0035 (0 hom., cov: 129)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC6 NM_005961.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

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 -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP7: Synonymous conserved (PhyloP=-3.2 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC6	NM_005961.3	c.5667C>G	p.Thr1889Thr	synonymous_variant	Exon 31 of 33	ENST00000421673.7	NP_005952.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC6	ENST00000421673.7	c.5667C>G	p.Thr1889Thr	synonymous_variant	Exon 31 of 33	5	NM_005961.3	ENSP00000406861.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 324 AN: 92610 Hom.: 0 Cov.: 129 FAILED QC

Gnomad AFR AF: 0.00209

Gnomad AMI AF: 0.00341

Gnomad AMR AF: 0.00576

Gnomad ASJ AF: 0.000900

Gnomad EAS AF: 0.00169

Gnomad SAS AF: 0.00354

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.00685

Gnomad NFE AF: 0.00343

Gnomad OTH AF: 0.00239

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1458256 Hom.: 0 Cov.: 320 AF XY: 0.00 AC XY: 0 AN XY: 725456

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00350 AC: 324 AN: 92656 Hom.: 0 Cov.: 129 AF XY: 0.00398 AC XY: 180 AN XY: 45188

Gnomad4 AFR AF: 0.00212

Gnomad4 AMR AF: 0.00575

Gnomad4 ASJ AF: 0.000900

Gnomad4 EAS AF: 0.00169

Gnomad4 SAS AF: 0.00355

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.00344

Gnomad4 OTH AF: 0.00158

Alfa AF: 0.0227 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.47

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: rs201950836; hg19: chr11-1017134;