Variant 4-70480984-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152291.3(MUC7):c.240C>G(p.Asn80Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,612,946 control chromosomes in the GnomAD database, including 54,480 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.26 ( 5472 hom., cov: 31)

Exomes 𝑓: 0.25 ( 49008 hom. )

Consequence

MUC7
NM_152291.3 missense

Scores

Clinical Significance

Not reported in ClinVar

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 Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0031020045).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MUC7	NM_152291.3 linkuse as main transcript	c.240C>G	p.Asn80Lys	missense_variant	3/3	ENST00000304887.6
MUC7	NM_001145006.2 linkuse as main transcript	c.240C>G	p.Asn80Lys	missense_variant	4/4
MUC7	NM_001145007.2 linkuse as main transcript	c.240C>G	p.Asn80Lys	missense_variant	4/4
MUC7	XM_047415723.1 linkuse as main transcript	c.240C>G	p.Asn80Lys	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC7	ENST00000304887.6 linkuse as main transcript	c.240C>G	p.Asn80Lys	missense_variant	3/3	1	NM_152291.3	P1

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

39856

AN:

151098

Hom.:

5466

Cov.:

show subpopulations

Gnomad AFR

AF:

0.295

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.246

Gnomad OTH

AF:

0.224

GnomAD3 exomes

AF:

0.265

AC:

66373

AN:

250254

Hom.:

9622

AF XY:

0.271

AC XY:

36654

AN XY:

135226

show subpopulations

Gnomad AFR exome

AF:

0.297

Gnomad AMR exome

AF:

0.153

Gnomad ASJ exome

AF:

0.203

Gnomad EAS exome

AF:

0.373

Gnomad SAS exome

AF:

0.373

Gnomad FIN exome

AF:

0.302

Gnomad NFE exome

AF:

0.249

Gnomad OTH exome

AF:

0.239

GnomAD4 exome

AF:

0.253

AC:

370246

AN:

1461728

Hom.:

49008

Cov.:

AF XY:

0.255

AC XY:

185584

AN XY:

727160

show subpopulations

Gnomad4 AFR exome

AF:

0.301

Gnomad4 AMR exome

AF:

0.158

Gnomad4 ASJ exome

AF:

0.204

Gnomad4 EAS exome

AF:

0.336

Gnomad4 SAS exome

AF:

0.367

Gnomad4 FIN exome

AF:

0.298

Gnomad4 NFE exome

AF:

0.243

Gnomad4 OTH exome

AF:

0.256

GnomAD4 genome

AF:

0.264

AC:

39881

AN:

151218

Hom.:

5472

Cov.:

AF XY:

0.267

AC XY:

19720

AN XY:

73842

show subpopulations

Gnomad4 AFR

AF:

0.295

Gnomad4 AMR

AF:

0.179

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.379

Gnomad4 SAS

AF:

0.377

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.246

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.232

Hom.:

3294

Bravo

AF:

0.252

TwinsUK

AF:

0.245

AC:

910

ALSPAC

AF:

0.242

AC:

933

ESP6500AA

AF:

0.300

AC:

1322

ESP6500EA

AF:

0.236

AC:

2029

ExAC

AF:

0.271

AC:

32930

Asia WGS

AF:

0.348

AC:

1211

AN:

3478

EpiCase

AF:

0.237

EpiControl

AF:

0.233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.018

DANN

Benign

0.14

DEOGEN2

Benign

0.010

T;.;T;T

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.0088

LIST_S2

Benign

0.32

T;T;.;.

MetaRNN

Benign

0.0031

T;T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.20

N;.;N;N

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.39

N;N;N;N

REVEL

Benign

0.15

Sift

Benign

0.51

T;T;T;T

Sift4G

Benign

1.0

T;T;T;T

Polyphen

0.0060

B;.;B;B

Vest4

0.016

MutPred

0.13

Gain of methylation at N80 (P = 0.0021);Gain of methylation at N80 (P = 0.0021);Gain of methylation at N80 (P = 0.0021);Gain of methylation at N80 (P = 0.0021);

MPC

0.060

ClinPred

0.00064

GERP RS

-3.1

Varity_R

0.025

gMVP

0.025

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over