NM_152291.3:c.655C>A

Variant names:

• chr4-70481399-C-A
• rs41454651
• NM_152291.3:c.655C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_152291.3(MUC7):​c.655C>A​(p.Pro219Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P219S) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 26)
• Consequence: MUC7 NM_152291.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.50
• Publications: 5 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.034585774).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152291.3. 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
	MUC7	NM_152291.3	MANE Select	c.655C>A	p.Pro219Thr	missense	Exon 3 of 3	NP_689504.2	Q8TAX7
	MUC7	NM_001145006.2		c.655C>A	p.Pro219Thr	missense	Exon 4 of 4	NP_001138478.1	Q8TAX7
	MUC7	NM_001145007.2		c.655C>A	p.Pro219Thr	missense	Exon 4 of 4	NP_001138479.1	Q8TAX7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUC7	ENST00000304887.6	TSL:1 MANE Select	c.655C>A	p.Pro219Thr	missense	Exon 3 of 3	ENSP00000302021.5	Q8TAX7
	MUC7	ENST00000413702.5	TSL:4	c.655C>A	p.Pro219Thr	missense	Exon 4 of 4	ENSP00000407422.1	Q8TAX7
	MUC7	ENST00000456088.5	TSL:4	c.655C>A	p.Pro219Thr	missense	Exon 4 of 4	ENSP00000400585.1	Q8TAX7

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 26

ExAC AF: 0.00000824 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.061
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.016
DANN	Benign	0.070
DEOGEN2	Benign	0.012	T
Eigen	Benign	-1.9
Eigen_PC	Benign	-2.0
FATHMM_MKL	Benign	0.0032	N
LIST_S2	Benign	0.46	T
M_CAP	Benign	0.0025	T
MetaRNN	Benign	0.035	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		-4.5
PrimateAI	Benign	0.34	T
PROVEAN	Benign	0.010	N
REVEL	Benign	0.020
Sift	Benign	0.77	T
Sift4G	Benign	0.44	T
Polyphen		0.0010	B
Vest4		0.092
MutPred		0.29		Loss of glycosylation at P219 (P = 0.0063)
MVP		0.16
MPC		0.027
ClinPred		0.027	T
GERP RS		-3.8
Varity_R		0.025
gMVP		0.051
Mutation Taster		=100/0	polymorphism

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: rs41454651; hg19: chr4-71347116;