Variant chr12-40441144-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_173600.2(MUC19):c.3705C>T(p.Asp1235=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00397 in 1,303,966 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0041 ( 20 hom. )

Consequence

MUC19
NM_173600.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.691

Variant links:

Genes affected

MUC19 (HGNC:14362): (mucin 19, oligomeric) This gene encodes a member of the gel-forming mucin protein family. Mucin family members are glycoproteins that have tandem repeats which are extensively O-glycosylated. The structural features of mucin proteins are responsible for the gel-like properties of mucus. The encoded protein may be involved in disruption of the ocular surface in Sjogren syndrome. [provided by RefSeq, Apr 2014]

MUC19 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 12-40441144-C-T is Benign according to our data. Variant chr12-40441144-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2642861.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.691 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUC19	NM_173600.2 linkuse as main transcript	c.3705C>T	p.Asp1235=	synonymous_variant	31/172
LOC105369736	XR_944868.3 linkuse as main transcript	n.74+2679G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUC19	ENST00000454784.10 linkuse as main transcript	c.3705C>T	p.Asp1235=	synonymous_variant	31/173	5		P1
	ENST00000552757.1 linkuse as main transcript	n.25+2679G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00317

AC:

482

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000965

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00373

Gnomad ASJ

AF:

0.00374

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00466

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00322

AC:

483

AN:

149898

Hom.:

AF XY:

0.00321

AC XY:

258

AN XY:

80486

show subpopulations

Gnomad AFR exome

AF:

0.00130

Gnomad AMR exome

AF:

0.00195

Gnomad ASJ exome

AF:

0.00393

Gnomad EAS exome

AF:

0.0000927

Gnomad SAS exome

AF:

0.00391

Gnomad FIN exome

AF:

0.000890

Gnomad NFE exome

AF:

0.00481

Gnomad OTH exome

AF:

0.00507

GnomAD4 exome

AF:

0.00408

AC:

4701

AN:

1151680

Hom.:

Cov.:

AF XY:

0.00407

AC XY:

2299

AN XY:

564676

show subpopulations

Gnomad4 AFR exome

AF:

0.00123

Gnomad4 AMR exome

AF:

0.00223

Gnomad4 ASJ exome

AF:

0.00452

Gnomad4 EAS exome

AF:

0.0000779

Gnomad4 SAS exome

AF:

0.00440

Gnomad4 FIN exome

AF:

0.000877

Gnomad4 NFE exome

AF:

0.00432

Gnomad4 OTH exome

AF:

0.00346

GnomAD4 genome

AF:

0.00316

AC:

481

AN:

152286

Hom.:

Cov.:

AF XY:

0.00303

AC XY:

226

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.000962

Gnomad4 AMR

AF:

0.00373

Gnomad4 ASJ

AF:

0.00374

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00581

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.00465

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00380

Hom.:

Bravo

AF:

0.00372

Asia WGS

AF:

0.00173

AC:

AN:

3478

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

Feb 01, 2023

MUC19: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

2.1

DANN

Benign

0.79

Splicing

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