Genetic Variant MUC15:c.*1220_*1229dupGTGTGTGTGT (chr11-26559835-T-TACACACACAC) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001135091.2(MUC15):c.*1220_*1229dupGTGTGTGTGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000019 ( 0 hom. )

Consequence

MUC15
NM_001135091.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.333

Publications

2 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.1220_1229dupGTGTGTGTGT	3_prime_UTR	Exon 5 of 5	NP_001128563.1	A0A0A0MT67
ANO3	NM_031418.4	MANE Select	c.1447+87_1447+96dupACACACACAC	intron	N/A	NP_113606.2	Q9BYT9-1
MUC15	NM_145650.4		c.1220_1229dupGTGTGTGTGT	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.1220_1229dupGTGTGTGTGT	3_prime_UTR	Exon 5 of 5	ENSP00000431983.1	A0A0A0MT67
ANO3	ENST00000256737.8	TSL:1 MANE Select	c.1447+87_1447+96dupACACACACAC	intron	N/A	ENSP00000256737.3	Q9BYT9-1
MUC15	ENST00000436318.6	TSL:5	c.1220_1229dupGTGTGTGTGT	3_prime_UTR	Exon 4 of 4	ENSP00000416753.2	A0A0A0MT67

Frequencies

GnomAD3 genomes

AF:

0.000160

AC:

AN:

144008

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000156

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000209

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000944

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000455

Gnomad OTH

AF:

0.00102

GnomAD4 exome

AF:

0.0000193

AC:

AN:

517834

Hom.:

Cov.:

AF XY:

0.0000142

AC XY:

AN XY:

281644

show subpopulations

African (AFR)

AF:

0.0000633

AC:

AN:

15802

American (AMR)

AF:

0.00

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:

0.0000383

AC:

AN:

52164

European-Finnish (FIN)

AF:

0.0000814

AC:

AN:

36854

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1942

European-Non Finnish (NFE)

AF:

0.0000132

AC:

AN:

303614

Other (OTH)

AF:

0.00

AC:

AN:

26748

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000160

AC:

AN:

144104

Hom.:

Cov.:

AF XY:

0.000200

AC XY:

AN XY:

69946

show subpopulations

African (AFR)

AF:

0.000156

AC:

AN:

38482

American (AMR)

AF:

0.000209

AC:

AN:

14380

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3382

East Asian (EAS)

AF:

0.00

AC:

AN:

4816

South Asian (SAS)

AF:

0.00

AC:

AN:

4424

European-Finnish (FIN)

AF:

0.000944

AC:

AN:

9538

Middle Eastern (MID)

AF:

0.00

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.0000455

AC:

AN:

65934

Other (OTH)

AF:

0.00101

AC:

AN:

1988

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.33

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over