rs1109501

Variant names:

• chr4-70463773-G-A
• rs1109501
• NM_001145006.2:c.-92-8442G>A

Variant summary

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

The NM_001145006.2(MUC7):​c.-92-8442G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,092 control chromosomes in the GnomAD database, including 4,686 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 0.23 (4686 hom., cov: 32)
• Consequence: MUC7 NM_001145006.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 14 publications found

Genes affected

MUC7 (HGNC:7518): (mucin 7, secreted) This gene encodes a small salivary mucin, which is thought to play a role in facilitating the clearance of bacteria in the oral cavity and to aid in mastication, speech, and swallowing. The central domain of this glycoprotein contains tandem repeats, each composed of 23 amino acids. This antimicrobial protein has antibacterial and antifungal activity. The most common allele contains 6 repeats, and some alleles may be associated with susceptibility to asthma. Alternatively spliced transcript variants with different 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Oct 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC7	NM_001145006.2	c.-92-8442G>A		intron_variant	Intron 1 of 3		NP_001138478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC7	ENST00000413702.5	c.-92-8442G>A		intron_variant	Intron 1 of 3	4		ENSP00000407422.1
MUC7	ENST00000515308.6	n.197-8442G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34629 AN: 151974 Hom.: 4677 Cov.: 32

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.228 AC: 34648 AN: 152092 Hom.: 4686 Cov.: 32 AF XY: 0.231 AC XY: 17154 AN XY: 74342

African (AFR) AF: 0.0955 AC: 3962 AN: 41502

American (AMR) AF: 0.274 AC: 4193 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2059 AN: 5158

South Asian (SAS) AF: 0.307 AC: 1479 AN: 4822

European-Finnish (FIN) AF: 0.234 AC: 2478 AN: 10568

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17851 AN: 67968

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.265 Hom.: 19695

Bravo AF: 0.227

Asia WGS AF: 0.343 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.81
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1109501; hg19: chr4-71329490;