Variant chr7-100995084-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001164462.2(MUC12):c.4521C>T(p.Phe1507Phe) 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.0043 ( 0 hom., cov: 6)

Exomes 𝑓: 0.0071 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MUC12
NM_001164462.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.38

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 -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BP6

Variant 7-100995084-C-T is Benign according to our data. Variant chr7-100995084-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2657810.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.38 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC12	NM_001164462.2 link	c.4521C>T	p.Phe1507Phe	synonymous_variant	2/12	ENST00000536621.6	NP_001157934.1	Q9UKN1-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC12	ENST00000536621.6 link	c.4521C>T	p.Phe1507Phe	synonymous_variant	2/12	5	NM_001164462.2	ENSP00000441929.1		Q9UKN1-2
MUC12	ENST00000379442.7 link	c.4950C>T	p.Phe1650Phe	synonymous_variant	5/15	5		ENSP00000368755.3		Q9UKN1-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

158

AN:

36906

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00158

Gnomad AMI

AF:

0.00385

Gnomad AMR

AF:

0.00233

Gnomad ASJ

AF:

0.00586

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00174

Gnomad FIN

AF:

0.00715

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00592

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00455

AC:

254

AN:

55774

Hom.:

AF XY:

0.00464

AC XY:

130

AN XY:

27988

show subpopulations

Gnomad AFR exome

AF:

0.000763

Gnomad AMR exome

AF:

0.00353

Gnomad ASJ exome

AF:

0.00200

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000492

Gnomad FIN exome

AF:

0.00668

Gnomad NFE exome

AF:

0.00888

Gnomad OTH exome

AF:

0.00467

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00707

AC:

4069

AN:

575644

Hom.:

Cov.:

AF XY:

0.00671

AC XY:

2013

AN XY:

299946

show subpopulations

Gnomad4 AFR exome

AF:

0.00158

Gnomad4 AMR exome

AF:

0.00229

Gnomad4 ASJ exome

AF:

0.00452

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000689

Gnomad4 FIN exome

AF:

0.0123

Gnomad4 NFE exome

AF:

0.00894

Gnomad4 OTH exome

AF:

0.00651

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00428

AC:

158

AN:

36948

Hom.:

Cov.:

AF XY:

0.00457

AC XY:

AN XY:

16184

show subpopulations

Gnomad4 AFR

AF:

0.00156

Gnomad4 AMR

AF:

0.00233

Gnomad4 ASJ

AF:

0.00586

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00174

Gnomad4 FIN

AF:

0.00715

Gnomad4 NFE

AF:

0.00592

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00174

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

MUC12: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.8

DANN

Benign

0.42

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