Variant 11-26559835-TACAC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001135091.2(MUC15):c.*1226_*1229del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 649,686 control chromosomes in the GnomAD database, including 2,231 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1760 hom., cov: 0)

Exomes 𝑓: 0.16 ( 471 hom. )

Consequence

MUC15
NM_001135091.2 3_prime_UTR

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.701

Variant links:

Genes affected

MUC15 (HGNC:14956): (mucin 15, cell surface associated) Predicted to be located in Golgi lumen and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

MUC15 links:

ANO3 (HGNC:14004): (anoctamin 3) The protein encoded by this gene belongs to the TMEM16 family of predicted membrane proteins, that are also known as anoctamins. While little is known about the function of this gene, mutations in this gene have been associated with some cases of autosomal dominant craniocervical dystonia. Cells from individuals with a mutation in this gene exhibited abnormalities in endoplasmic reticulum-dependent calcium signaling. Studies in rat show that the rat ortholog of this protein interacts with, and modulates the activity of a sodium-activated potassium channel. Deletion of this gene caused increased pain sensitivity in the rat model system. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2015]

ANO3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 11-26559835-TACAC-T is Benign according to our data. Variant chr11-26559835-TACAC-T is described in ClinVar as [Benign]. Clinvar id is 1243722.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUC15	NM_001135091.2 linkuse as main transcript	c.1226_1229del		3_prime_UTR_variant	5/5	ENST00000529533.6	NP_001128563.1
ANO3	NM_031418.4 linkuse as main transcript	c.1447+93_1447+96del		intron_variant		ENST00000256737.8	NP_113606.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUC15	ENST00000529533.6 linkuse as main transcript	c.1226_1229del		3_prime_UTR_variant	5/5	1	NM_001135091.2	ENSP00000431983
ANO3	ENST00000256737.8 linkuse as main transcript	c.1447+93_1447+96del		intron_variant		1	NM_031418.4	ENSP00000256737	P3	Q9BYT9-1

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

21978

AN:

143802

Hom.:

1762

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0911

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.170

GnomAD4 exome

AF:

0.157

AC:

79232

AN:

505788

Hom.:

471

AF XY:

0.158

AC XY:

43387

AN XY:

274890

show subpopulations

Gnomad4 AFR exome

AF:

0.0945

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.131

Gnomad4 EAS exome

AF:

0.165

Gnomad4 SAS exome

AF:

0.143

Gnomad4 FIN exome

AF:

0.159

Gnomad4 NFE exome

AF:

0.166

Gnomad4 OTH exome

AF:

0.159

GnomAD4 genome

AF:

0.153

AC:

21997

AN:

143898

Hom.:

1760

Cov.:

AF XY:

0.153

AC XY:

10670

AN XY:

69840

show subpopulations

Gnomad4 AFR

AF:

0.0911

Gnomad4 AMR

AF:

0.140

Gnomad4 ASJ

AF:

0.136

Gnomad4 EAS

AF:

0.158

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.162

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.171

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 06, 2019

- -

Dystonia 24

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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