dbSNP rs79635145: MUC12:p.Ser4565Ser (chr7-101004258-C-T) – 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_001164462.2(MUC12):c.13695C>T(p.Ser4565Ser) 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 0.57 ( 473 hom., cov: 3)

Exomes 𝑓: 0.64 ( 83552 hom. )

Failed GnomAD Quality Control

Consequence

MUC12
NM_001164462.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.91

Variant links:

Genes affected

MUC12 (HGNC:7510): (mucin 12, cell surface associated) This gene encodes an integral membrane glycoprotein that is a member of the mucin family. Mucins are O-glycosylated proteins that play an essential role in forming protective mucous barriers on epithelial surfaces and have been implicated in epithelial renewal and differentiation. These glycoproteins also play a role in intracellular signaling. This protein is expressed on the apical membrane surface of epithelial cells that line the mucosal surfaces of many different tissues including the colon, pancreas, prostate, and uterus. The expression of this gene is downregulated in colorectal cancer tissue. [provided by RefSeq, Apr 2017]

MUC12 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=-0.98).

BP6

Variant 7-101004258-C-T is Benign according to our data. Variant chr7-101004258-C-T is described in ClinVar as [Benign]. Clinvar id is 403116.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.91 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC12	NM_001164462.2 link	c.13695C>T	p.Ser4565Ser	synonymous_variant	Exon 2 of 12	ENST00000536621.6	NP_001157934.1	Q9UKN1-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC12	ENST00000536621.6 link	c.13695C>T	p.Ser4565Ser	synonymous_variant	Exon 2 of 12	5	NM_001164462.2	ENSP00000441929.1		Q9UKN1-2
MUC12	ENST00000379442.7 link	c.14124C>T	p.Ser4708Ser	synonymous_variant	Exon 5 of 15	5		ENSP00000368755.3		Q9UKN1-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

1191

AN:

2086

Hom.:

473

Cov.:

FAILED QC

Gnomad AFR

AF:

0.582

Gnomad AMI

AF:

0.556

Gnomad AMR

AF:

0.690

Gnomad ASJ

AF:

0.609

Gnomad EAS

AF:

0.778

Gnomad SAS

AF:

0.637

Gnomad FIN

AF:

0.500

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.538

Gnomad OTH

AF:

0.636

GnomAD3 exomes

AF:

0.751

AC:

40691

AN:

54170

Hom.:

15365

AF XY:

0.752

AC XY:

20455

AN XY:

27194

show subpopulations

Gnomad AFR exome

AF:

0.736

Gnomad AMR exome

AF:

0.792

Gnomad ASJ exome

AF:

0.744

Gnomad EAS exome

AF:

0.815

Gnomad SAS exome

AF:

0.721

Gnomad FIN exome

AF:

0.684

Gnomad NFE exome

AF:

0.723

Gnomad OTH exome

AF:

0.761

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.636

AC:

283155

AN:

445316

Hom.:

83552

Cov.:

AF XY:

0.636

AC XY:

143557

AN XY:

225548

show subpopulations

Gnomad4 AFR exome

AF:

0.671

Gnomad4 AMR exome

AF:

0.740

Gnomad4 ASJ exome

AF:

0.673

Gnomad4 EAS exome

AF:

0.773

Gnomad4 SAS exome

AF:

0.611

Gnomad4 FIN exome

AF:

0.636

Gnomad4 NFE exome

AF:

0.617

Gnomad4 OTH exome

AF:

0.662

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.572

AC:

1193

AN:

2084

Hom.:

473

Cov.:

AF XY:

0.563

AC XY:

526

AN XY:

934

show subpopulations

Gnomad4 AFR

AF:

0.585

Gnomad4 AMR

AF:

0.695

Gnomad4 ASJ

AF:

0.609

Gnomad4 EAS

AF:

0.778

Gnomad4 SAS

AF:

0.653

Gnomad4 FIN

AF:

0.500

Gnomad4 NFE

AF:

0.538

Gnomad4 OTH

AF:

0.625

Alfa

AF:

0.711

Hom.:

3380

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 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

-0.98

CADD

Benign

1.6

DANN

Benign

0.19

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