11-1201105-A-G

Variant names:

• chr11-1201105-A-G
• rs13380
• NM_001304359.2:c.*403A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001304359.2(MUC5AC):​c.*403A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 177,988 control chromosomes in the GnomAD database, including 2,747 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 0.16 (2235 hom., cov: 33)
  • Exomes 𝑓: 0.18 (512 hom.)
• Consequence: MUC5AC NM_001304359.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.73
• Publications: 4 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 (Cadd=0.046).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC5AC	NM_001304359.2	MANE Select	c.*403A>G		3_prime_UTR	Exon 49 of 49	NP_001291288.1	P98088

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC5AC	ENST00000621226.2	TSL:5 MANE Select	c.*403A>G		3_prime_UTR	Exon 49 of 49	ENSP00000485659.1	P98088

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24601 AN: 152028 Hom.: 2235 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0591

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.181 AC: 4679 AN: 25842 Hom.: 512 Cov.: 0 AF XY: 0.182 AC XY: 2375 AN XY: 13044

African (AFR) AF: 0.125 AC: 138 AN: 1102

American (AMR) AF: 0.109 AC: 146 AN: 1344

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 87 AN: 1004

East Asian (EAS) AF: 0.00824 AC: 14 AN: 1698

South Asian (SAS) AF: 0.0676 AC: 25 AN: 370

European-Finnish (FIN) AF: 0.278 AC: 305 AN: 1098

Middle Eastern (MID) AF: 0.116 AC: 13 AN: 112

European-Non Finnish (NFE) AF: 0.211 AC: 3684 AN: 17492

Other (OTH) AF: 0.165 AC: 267 AN: 1622

GnomAD4 genome AF: 0.162 AC: 24597 AN: 152146 Hom.: 2235 Cov.: 33 AF XY: 0.161 AC XY: 12009 AN XY: 74378

African (AFR) AF: 0.128 AC: 5324 AN: 41532

American (AMR) AF: 0.130 AC: 1995 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0721 AC: 250 AN: 3468

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5190

South Asian (SAS) AF: 0.0594 AC: 286 AN: 4818

European-Finnish (FIN) AF: 0.270 AC: 2854 AN: 10564

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13324 AN: 67958

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.178 Hom.: 294

Bravo AF: 0.151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.046
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs13380;