Genetic Variant NM_018406.7:c.3723A>T (chr3-195787857-T-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_018406.7(MUC4):c.3723A>T(p.Ala1241Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 109 hom., cov: 1)

Exomes 𝑓: 0.45 ( 51911 hom. )

Failed GnomAD Quality Control

Consequence

MUC4
NM_018406.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.319

Variant links:

Genes affected

MUC4 (HGNC:7514): (mucin 4, cell surface associated) The major constituents of mucus, the viscous secretion that covers epithelial surfaces such as those in the trachea, colon, and cervix, are highly glycosylated proteins called mucins. These glycoproteins play important roles in the protection of the epithelial cells and have been implicated in epithelial renewal and differentiation. This gene encodes an integral membrane glycoprotein found on the cell surface, although secreted isoforms may exist. At least two dozen transcript variants of this gene have been found, although for many of them the full-length transcript has not been determined or they are found only in tumor tissues. This gene contains a region in the coding sequence which has a variable number (>100) of 48 nt tandem repeats. [provided by RefSeq, Jul 2008]

MUC4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 3-195787857-T-A is Benign according to our data. Variant chr3-195787857-T-A is described in ClinVar as [Benign]. Clinvar id is 403123.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.319 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC4	NM_018406.7 link	c.3723A>T	p.Ala1241Ala	synonymous_variant	Exon 2 of 25	ENST00000463781.8	NP_060876.5	Q99102-1E9PDY6
MUC4	NM_004532.6 link	c.83-9402A>T		intron_variant	Intron 1 of 23		NP_004523.3	Q99102-13A0T3F4
MUC4	NM_138297.5 link	c.83-13552A>T		intron_variant	Intron 1 of 22		NP_612154.2	Q99102-12A0T3F4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC4	ENST00000463781.8 link	c.3723A>T	p.Ala1241Ala	synonymous_variant	Exon 2 of 25	5	NM_018406.7	ENSP00000417498.3		Q99102-1E9PDY6

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

650

AN:

5590

Hom.:

109

Cov.:

FAILED QC

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.0649

Gnomad FIN

AF:

0.144

Gnomad MID

AF:

0.0556

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.171

GnomAD3 exomes

AF:

0.362

AC:

16147

AN:

44546

Hom.:

3382

AF XY:

0.362

AC XY:

8160

AN XY:

22552

show subpopulations

Gnomad AFR exome

AF:

0.386

Gnomad AMR exome

AF:

0.258

Gnomad ASJ exome

AF:

0.452

Gnomad EAS exome

AF:

0.544

Gnomad SAS exome

AF:

0.288

Gnomad FIN exome

AF:

0.413

Gnomad NFE exome

AF:

0.366

Gnomad OTH exome

AF:

0.382

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.450

AC:

189356

AN:

420360

Hom.:

51911

Cov.:

AF XY:

0.449

AC XY:

99220

AN XY:

220772

show subpopulations

Gnomad4 AFR exome

AF:

0.423

Gnomad4 AMR exome

AF:

0.323

Gnomad4 ASJ exome

AF:

0.561

Gnomad4 EAS exome

AF:

0.663

Gnomad4 SAS exome

AF:

0.382

Gnomad4 FIN exome

AF:

0.511

Gnomad4 NFE exome

AF:

0.439

Gnomad4 OTH exome

AF:

0.469

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.116

AC:

650

AN:

5586

Hom.:

109

Cov.:

AF XY:

0.117

AC XY:

304

AN XY:

2602

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.107

Gnomad4 ASJ

AF:

0.183

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.0644

Gnomad4 FIN

AF:

0.144

Gnomad4 NFE

AF:

0.111

Gnomad4 OTH

AF:

0.171

Alfa

AF:

0.0683

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.5

DANN

Benign

0.37

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