Variant chr7-100992405-G-A 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.1842G>A(p.Ser614=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00316 in 151,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 0 hom., cov: 36)

Exomes 𝑓: 0.0024 ( 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: -4.00

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 7-100992405-G-A is Benign according to our data. Variant chr7-100992405-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657800.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-4 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC12	NM_001164462.2 linkuse as main transcript	c.1842G>A	p.Ser614=	synonymous_variant	2/12	ENST00000536621.6	NP_001157934.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC12	ENST00000536621.6 linkuse as main transcript	c.1842G>A	p.Ser614=	synonymous_variant	2/12	5	NM_001164462.2	ENSP00000441929	A2	Q9UKN1-2
MUC12	ENST00000379442.7 linkuse as main transcript	c.2271G>A	p.Ser757=	synonymous_variant	5/15	5		ENSP00000368755	P4	Q9UKN1-1

Frequencies

GnomAD3 genomes

AF:

0.00317

AC:

480

AN:

151558

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000556

Gnomad AMI

AF:

0.00885

Gnomad AMR

AF:

0.000525

Gnomad ASJ

AF:

0.00174

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00351

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00271

AC:

397

AN:

146544

Hom.:

AF XY:

0.00266

AC XY:

207

AN XY:

77702

show subpopulations

Gnomad AFR exome

AF:

0.000621

Gnomad AMR exome

AF:

0.000365

Gnomad ASJ exome

AF:

0.00201

Gnomad EAS exome

AF:

0.000188

Gnomad SAS exome

AF:

0.0000440

Gnomad FIN exome

AF:

0.0211

Gnomad NFE exome

AF:

0.00324

Gnomad OTH exome

AF:

0.00385

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00236

AC:

3254

AN:

1379200

Hom.:

Cov.:

193

AF XY:

0.00236

AC XY:

1606

AN XY:

680476

show subpopulations

Gnomad4 AFR exome

AF:

0.000443

Gnomad4 AMR exome

AF:

0.000532

Gnomad4 ASJ exome

AF:

0.00195

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.0000884

Gnomad4 FIN exome

AF:

0.0210

Gnomad4 NFE exome

AF:

0.00215

Gnomad4 OTH exome

AF:

0.00221

GnomAD4 genome

AF:

0.00316

AC:

480

AN:

151676

Hom.:

Cov.:

AF XY:

0.00363

AC XY:

269

AN XY:

74130

show subpopulations

Gnomad4 AFR

AF:

0.000554

Gnomad4 AMR

AF:

0.000524

Gnomad4 ASJ

AF:

0.00174

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.0185

Gnomad4 NFE

AF:

0.00351

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00454

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

Jul 01, 2022

MUC12: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

6.3

DANN

Benign

0.47

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