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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001135091.2(MUC15):c.*1224_*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 0.0372 in 656,772 control chromosomes in the GnomAD database, including 72 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 61 hom., cov: 0)

Exomes 𝑓: 0.042 ( 11 hom. )

Consequence

MUC15
NM_001135091.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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 -10 ACMG points.

BP6

Variant 11-26559835-TACACAC-T is Benign according to our data. Variant chr11-26559835-TACACAC-T is described in ClinVar as [Benign]. Clinvar id is 1240657.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0564 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.1224_1229del		3_prime_UTR_variant	5/5	ENST00000529533.6	NP_001128563.1
ANO3	NM_031418.4 linkuse as main transcript	c.1447+91_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.1224_1229del		3_prime_UTR_variant	5/5	1	NM_001135091.2	ENSP00000431983
ANO3	ENST00000256737.8 linkuse as main transcript	c.1447+91_1447+96del		intron_variant		1	NM_031418.4	ENSP00000256737	P3	Q9BYT9-1

Frequencies

GnomAD3 genomes

AF:

0.0191

AC:

2751

AN:

143924

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0581

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00857

Gnomad ASJ

AF:

0.00118

Gnomad EAS

AF:

0.00476

Gnomad SAS

AF:

0.0185

Gnomad FIN

AF:

0.00158

Gnomad MID

AF:

0.0135

Gnomad NFE

AF:

0.00370

Gnomad OTH

AF:

0.0137

GnomAD4 exome

AF:

0.0422

AC:

21663

AN:

512752

Hom.:

AF XY:

0.0427

AC XY:

11920

AN XY:

278852

show subpopulations

Gnomad4 AFR exome

AF:

0.0591

Gnomad4 AMR exome

AF:

0.0306

Gnomad4 ASJ exome

AF:

0.0320

Gnomad4 EAS exome

AF:

0.0423

Gnomad4 SAS exome

AF:

0.0495

Gnomad4 FIN exome

AF:

0.0340

Gnomad4 NFE exome

AF:

0.0431

Gnomad4 OTH exome

AF:

0.0416

GnomAD4 genome

AF:

0.0192

AC:

2768

AN:

144020

Hom.:

Cov.:

AF XY:

0.0191

AC XY:

1333

AN XY:

69904

show subpopulations

Gnomad4 AFR

AF:

0.0584

Gnomad4 AMR

AF:

0.00856

Gnomad4 ASJ

AF:

0.00118

Gnomad4 EAS

AF:

0.00478

Gnomad4 SAS

AF:

0.0190

Gnomad4 FIN

AF:

0.00158

Gnomad4 NFE

AF:

0.00370

Gnomad4 OTH

AF:

0.0126

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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