chr11-26189234-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001313726.2(ANO3):c.58C>T(p.His20Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0131 in 984,950 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001313726.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANO3 | NM_001313726.2 | c.58C>T | p.His20Tyr | missense_variant | Exon 1 of 28 | NP_001300655.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANO3 | ENST00000672621.1 | c.58C>T | p.His20Tyr | missense_variant | Exon 1 of 28 | ENSP00000500506.1 | ||||
ANO3 | ENST00000531798.1 | n.112C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0103 AC: 1571AN: 152118Hom.: 11 Cov.: 32
GnomAD4 exome AF: 0.0137 AC: 11377AN: 832714Hom.: 76 Cov.: 29 AF XY: 0.0138 AC XY: 5303AN XY: 384546
GnomAD4 genome AF: 0.0103 AC: 1571AN: 152236Hom.: 10 Cov.: 32 AF XY: 0.0107 AC XY: 796AN XY: 74426
ClinVar
Submissions by phenotype
Dystonia 24 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | May 20, 2023 | The observed missense c.58C>T (p.His20Tyr) variant in ANO3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.His20Tyr variant is absent in gnomAD Exomes. This variant has not been submitted to the ClinVar database. The amino acid His at position 20 is changed to a Tyr changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance (VUS). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at