rs71047866

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001135091.2(MUC15):c.*1202_*1229delGTGTGTGTGTGTGTGTGTGTGTGTGTGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 517,838 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0000019 ( 0 hom. )

Consequence

MUC15
NM_001135091.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.701

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

dystonia 24
Inheritance: AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P, Orphanet

ANO3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135091.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MUC15	NM_001135091.2	MANE Select	c.1202_1229delGTGTGTGTGTGTGTGTGTGTGTGTGTGT	3_prime_UTR	Exon 5 of 5	NP_001128563.1	A0A0A0MT67
ANO3	NM_031418.4	MANE Select	c.1447+69_1447+96delACACACACACACACACACACACACACAC	intron	N/A	NP_113606.2	Q9BYT9-1
MUC15	NM_145650.4		c.1202_1229delGTGTGTGTGTGTGTGTGTGTGTGTGTGT	3_prime_UTR	Exon 4 of 4	NP_663625.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MUC15	ENST00000529533.6	TSL:1 MANE Select	c.1202_1229delGTGTGTGTGTGTGTGTGTGTGTGTGTGT	3_prime_UTR	Exon 5 of 5	ENSP00000431983.1	A0A0A0MT67
ANO3	ENST00000256737.8	TSL:1 MANE Select	c.1447+69_1447+96delACACACACACACACACACACACACACAC	intron	N/A	ENSP00000256737.3	Q9BYT9-1
MUC15	ENST00000436318.6	TSL:5	c.1202_1229delGTGTGTGTGTGTGTGTGTGTGTGTGTGT	3_prime_UTR	Exon 4 of 4	ENSP00000416753.2	A0A0A0MT67

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000193

AC:

AN:

517838

Hom.:

AF XY:

0.00000355

AC XY:

AN XY:

281644

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

15804

American (AMR)

AF:

0.0000286

AC:

AN:

35004

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15000

East Asian (EAS)

AF:

0.00

AC:

AN:

30706

South Asian (SAS)

AF:

0.00

AC:

AN:

52164

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36858

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1942

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

303612

Other (OTH)

AF:

0.00

AC:

AN:

26748

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over