11-22193331-A-AAGGAGGAGGGGAATGAGGAGGAGG
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_213599.3(ANO5):c.-156_-155insAGGGGAATGAGGAGGAGGAGGAGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.82 ( 50911 hom., cov: 0)
Exomes 𝑓: 0.79 ( 394924 hom. )
Failed GnomAD Quality Control
Consequence
ANO5
NM_213599.3 5_prime_UTR
NM_213599.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.16
Genes affected
ANO5 (HGNC:27337): (anoctamin 5) This gene encodes a member of the anoctamin family of transmembrane proteins. The encoded protein is likely a calcium activated chloride channel. Mutations in this gene have been associated with gnathodiaphyseal dysplasia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant 11-22193331-A-AAGGAGGAGGGGAATGAGGAGGAGG is Benign according to our data. Variant chr11-22193331-A-AAGGAGGAGGGGAATGAGGAGGAGG is described in ClinVar as [Benign]. Clinvar id is 304093.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANO5 | NM_213599.3 | c.-156_-155insAGGGGAATGAGGAGGAGGAGGAGG | 5_prime_UTR_variant | 1/22 | ENST00000324559.9 | NP_998764.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANO5 | ENST00000324559.9 | c.-156_-155insAGGGGAATGAGGAGGAGGAGGAGG | 5_prime_UTR_variant | 1/22 | 1 | NM_213599.3 | ENSP00000315371 | P2 |
Frequencies
GnomAD3 genomes AF: 0.819 AC: 123203AN: 150488Hom.: 50858 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.787 AC: 999937AN: 1270584Hom.: 394924 Cov.: 57 AF XY: 0.786 AC XY: 484315AN XY: 616144
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.819 AC: 123317AN: 150606Hom.: 50911 Cov.: 0 AF XY: 0.816 AC XY: 59991AN XY: 73484
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Limb-girdle muscular dystrophy, recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Gnathodiaphyseal dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Miyoshi myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at