11-26559835-TACACACACACACACACAC-TACACACACACACACACACACACACAC

Variant names:

• chr11-26559835-T-TACACACAC
• rs71047866
• NM_001135091.2:c.*1222_*1229dupGTGTGTGT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001135091.2(MUC15):​c.*1222_*1229dupGTGTGTGT 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 0.00044 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00014 (0 hom.)
• Consequence: MUC15 NM_001135091.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

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]

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC15	NM_001135091.2	c.*1222_*1229dupGTGTGTGT		3_prime_UTR_variant	Exon 5 of 5	ENST00000529533.6	NP_001128563.1
ANO3	NM_031418.4	c.1447+89_1447+96dupACACACAC		intron_variant	Intron 14 of 26	ENST00000256737.8	NP_113606.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC15	ENST00000529533	c.*1222_*1229dupGTGTGTGT		3_prime_UTR_variant	Exon 5 of 5	1	NM_001135091.2	ENSP00000431983.1
ANO3	ENST00000256737.8	c.1447+89_1447+96dupACACACAC		intron_variant	Intron 14 of 26	1	NM_031418.4	ENSP00000256737.3

Frequencies

GnomAD3 genomes AF: 0.000444 AC: 64 AN: 144006 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000209

Gnomad ASJ AF: 0.00177

Gnomad EAS AF: 0.000414

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00676

Gnomad NFE AF: 0.000121

Gnomad OTH AF: 0.000508

GnomAD4 exome AF: 0.000145 AC: 75 AN: 517806 Hom.: 0 Cov.: 0 AF XY: 0.000153 AC XY: 43 AN XY: 281628

Gnomad4 AFR exome AF: 0.000759

Gnomad4 AMR exome AF: 0.000114

Gnomad4 ASJ exome AF: 0.000333

Gnomad4 EAS exome AF: 0.000130

Gnomad4 SAS exome AF: 0.000268

Gnomad4 FIN exome AF: 0.0000543

Gnomad4 NFE exome AF: 0.000105

Gnomad4 OTH exome AF: 0.0000748

GnomAD4 genome AF: 0.000444 AC: 64 AN: 144102 Hom.: 0 Cov.: 0 AF XY: 0.000500 AC XY: 35 AN XY: 69946

Gnomad4 AFR AF: 0.00109

Gnomad4 AMR AF: 0.000209

Gnomad4 ASJ AF: 0.00177

Gnomad4 EAS AF: 0.000415

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000121

Gnomad4 OTH AF: 0.000503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71047866; hg19: chr11-26581382;