Variant 3-195725761-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001282506.2(MUC20):c.1158C>T(p.Ser386=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,393,264 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 0.0052 ( 0 hom., cov: 17)

Exomes 𝑓: 0.0019 ( 0 hom. )

Consequence

MUC20
NM_001282506.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.627

Variant links:

Genes affected

MUC20 (HGNC:23282): (mucin 20, cell surface associated) This gene encodes a member of the mucin protein family. Mucins are high molecular weight glycoproteins secreted by many epithelial tissues to form an insoluble mucous barrier. The C-terminus of this family member associates with the multifunctional docking site of the MET proto-oncogene and suppresses activation of some downstream MET signaling cascades. The protein features a mucin tandem repeat domain that varies between two and six copies in most individuals. Multiple variants encoding different isoforms have been found for this gene. A related pseudogene, which is also located on chromosome 3, has been identified. [provided by RefSeq, Apr 2014]

MUC20 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 3-195725761-C-T is Benign according to our data. Variant chr3-195725761-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2654370.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.627 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC20	NM_001282506.2 linkuse as main transcript	c.1158C>T	p.Ser386=	synonymous_variant	2/4	ENST00000447234.7	NP_001269435.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC20	ENST00000447234.7 linkuse as main transcript	c.1158C>T	p.Ser386=	synonymous_variant	2/4	5	NM_001282506.2	ENSP00000414350	A2	Q8N307-1
MUC20	ENST00000436408.6 linkuse as main transcript	c.1158C>T	p.Ser386=	synonymous_variant	2/4	5		ENSP00000396774	A2
MUC20	ENST00000445522.6 linkuse as main transcript	c.1053C>T	p.Ser351=	synonymous_variant	1/3	2		ENSP00000405629	P4	Q8N307-3

Frequencies

GnomAD3 genomes

AF:

0.00524

AC:

683

AN:

130240

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00300

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00352

Gnomad ASJ

AF:

0.000308

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00401

Gnomad FIN

AF:

0.0161

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00632

Gnomad OTH

AF:

0.00233

GnomAD3 exomes

AF:

0.00155

AC:

214

AN:

138024

Hom.:

AF XY:

0.00148

AC XY:

107

AN XY:

72244

show subpopulations

Gnomad AFR exome

AF:

0.00112

Gnomad AMR exome

AF:

0.000547

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000427

Gnomad FIN exome

AF:

0.00870

Gnomad NFE exome

AF:

0.00110

Gnomad OTH exome

AF:

0.00176

GnomAD4 exome

AF:

0.00190

AC:

2403

AN:

1262918

Hom.:

Cov.:

AF XY:

0.00209

AC XY:

1321

AN XY:

632696

show subpopulations

Gnomad4 AFR exome

AF:

0.00117

Gnomad4 AMR exome

AF:

0.00131

Gnomad4 ASJ exome

AF:

0.000369

Gnomad4 EAS exome

AF:

0.0000262

Gnomad4 SAS exome

AF:

0.00269

Gnomad4 FIN exome

AF:

0.00985

Gnomad4 NFE exome

AF:

0.00159

Gnomad4 OTH exome

AF:

0.00194

GnomAD4 genome

AF:

0.00524

AC:

683

AN:

130346

Hom.:

Cov.:

AF XY:

0.00523

AC XY:

328

AN XY:

62744

show subpopulations

Gnomad4 AFR

AF:

0.00299

Gnomad4 AMR

AF:

0.00352

Gnomad4 ASJ

AF:

0.000308

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00401

Gnomad4 FIN

AF:

0.0161

Gnomad4 NFE

AF:

0.00632

Gnomad4 OTH

AF:

0.00230

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

Mar 01, 2023

MUC20: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.0

DANN

Benign

0.61

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