11-1193830-G-C

Variant names:

• chr11-1193830-G-C
• rs2075842
• NM_001304359.2:c.14755+171G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304359.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC5AC	NM_001304359.2	MANE Select	c.14755+171G>C		intron	N/A	NP_001291288.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC5AC	ENST00000621226.2	TSL:5 MANE Select	c.14755+171G>C		intron	N/A	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

African (AFR) AF: 0.661 AC: 27454 AN: 41544

American (AMR) AF: 0.424 AC: 6482 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1043 AN: 3472

East Asian (EAS) AF: 0.307 AC: 1583 AN: 5150

South Asian (SAS) AF: 0.439 AC: 2118 AN: 4824

European-Finnish (FIN) AF: 0.456 AC: 4842 AN: 10616

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27307 AN: 67976

Other (OTH) AF: 0.453 AC: 957 AN: 2114

Alfa AF: 0.290 Hom.: 676

Bravo AF: 0.478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.32
PhyloP100		-1.7

Splicing

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

Other links and lift over

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