Genetic Variant MUC7:p.Lys83GlnfsTer10 (chr4-70480983-A-AC) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_152291.3(MUC7):c.246dupC(p.Lys83GlnfsTer10) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00274 in 1,613,468 control chromosomes in the GnomAD database, including 17 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 4 hom., cov: 31)

Exomes 𝑓: 0.0027 ( 13 hom. )

Consequence

MUC7
NM_152291.3 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.88

Variant links:

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]

MUC7 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 4-70480983-A-AC is Benign according to our data. Variant chr4-70480983-A-AC is described in ClinVar as [Likely_benign]. Clinvar id is 3770400.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC7	NM_152291.3 link	c.246dupC	p.Lys83GlnfsTer10	frameshift_variant	Exon 3 of 3	ENST00000304887.6	NP_689504.2	Q8TAX7
MUC7	NM_001145006.2 link	c.246dupC	p.Lys83GlnfsTer10	frameshift_variant	Exon 4 of 4		NP_001138478.1	Q8TAX7
MUC7	NM_001145007.2 link	c.246dupC	p.Lys83GlnfsTer10	frameshift_variant	Exon 4 of 4		NP_001138479.1	Q8TAX7
MUC7	XM_047415723.1 link	c.246dupC	p.Lys83GlnfsTer10	frameshift_variant	Exon 4 of 4		XP_047271679.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC7	ENST00000304887.6 link	c.246dupC	p.Lys83GlnfsTer10	frameshift_variant	Exon 3 of 3	1	NM_152291.3	ENSP00000302021.5		Q8TAX7

Frequencies

GnomAD3 genomes

AF:

0.00284

AC:

431

AN:

151548

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000291

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000658

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.0130

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00382

Gnomad OTH

AF:

0.00240

GnomAD3 exomes

AF:

0.00284

AC:

713

AN:

251254

Hom.:

AF XY:

0.00298

AC XY:

405

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.000578

Gnomad ASJ exome

AF:

0.00189

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.0121

Gnomad NFE exome

AF:

0.00335

Gnomad OTH exome

AF:

0.00408

GnomAD4 exome

AF:

0.00273

AC:

3985

AN:

1461802

Hom.:

Cov.:

AF XY:

0.00284

AC XY:

2062

AN XY:

727204

show subpopulations

Gnomad4 AFR exome

AF:

0.000299

Gnomad4 AMR exome

AF:

0.000671

Gnomad4 ASJ exome

AF:

0.00199

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000139

Gnomad4 FIN exome

AF:

0.0131

Gnomad4 NFE exome

AF:

0.00270

Gnomad4 OTH exome

AF:

0.00288

GnomAD4 genome

AF:

0.00284

AC:

430

AN:

151666

Hom.:

Cov.:

AF XY:

0.00333

AC XY:

247

AN XY:

74112

show subpopulations

Gnomad4 AFR

AF:

0.000291

Gnomad4 AMR

AF:

0.000657

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000209

Gnomad4 FIN

AF:

0.0130

Gnomad4 NFE

AF:

0.00380

Gnomad4 OTH

AF:

0.00238

Alfa

AF:

0.00565

Hom.:

Bravo

AF:

0.00162

EpiCase

AF:

0.00300

EpiControl

AF:

0.00225

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MUC7: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over