11-1193830-G-C

Position:

• chr11-1193830-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304359.2(MUC5AC):​c.14755+171G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,204 control chromosomes in the GnomAD database, including 18,198 homozygotes. 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 0.47 (18198 hom., cov: 35)
• Consequence: MUC5AC NM_001304359.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

MUC5AC (HGNC:7515): (mucin 5AC, oligomeric mucus/gel-forming) Predicted to be an extracellular matrix structural constituent. Involved in phosphatidylinositol-mediated signaling. Located in cytoplasm; extracellular space; and mucus layer. Implicated in dry eye syndrome. Biomarker of several diseases, including Sjogren's syndrome; biliary tract disease (multiple); cystic fibrosis; eye disease (multiple); and pancreatic cancer (multiple). [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC5AC	NM_001304359.2	c.14755+171G>C		intron_variant		ENST00000621226.2	NP_001291288.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC5AC	ENST00000621226.2	c.14755+171G>C		intron_variant		5	NM_001304359.2	ENSP00000485659.1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72186 AN: 152086 Hom.: 18164 Cov.: 35

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.450

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.475 AC: 72281 AN: 152204 Hom.: 18198 Cov.: 35 AF XY: 0.477 AC XY: 35518 AN XY: 74420

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.453

Alfa AF: 0.290 Hom.: 676

Bravo AF: 0.478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2075842; hg19: chr11-1215056; COSMIC: COSV64369164;