chr11-26634298-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_031418.4(ANO3):c.1968C>T(p.Ile656=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00788 in 1,611,710 control chromosomes in the GnomAD database, including 90 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. I656I) has been classified as Uncertain significance.
Frequency
Consequence
NM_031418.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO3 | NM_031418.4 | c.1968C>T | p.Ile656= | synonymous_variant | 19/27 | ENST00000256737.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO3 | ENST00000256737.8 | c.1968C>T | p.Ile656= | synonymous_variant | 19/27 | 1 | NM_031418.4 | P3 | |
ANO3 | ENST00000672621.1 | c.2151C>T | p.Ile717= | synonymous_variant | 20/28 | ||||
ANO3 | ENST00000525139.5 | c.1920C>T | p.Ile640= | synonymous_variant | 19/27 | 5 | |||
ANO3 | ENST00000531568.1 | c.1530C>T | p.Ile510= | synonymous_variant | 16/24 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00575 AC: 875AN: 152068Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00632 AC: 1585AN: 250898Hom.: 9 AF XY: 0.00644 AC XY: 873AN XY: 135620
GnomAD4 exome AF: 0.00810 AC: 11822AN: 1459524Hom.: 86 Cov.: 29 AF XY: 0.00780 AC XY: 5664AN XY: 726228
GnomAD4 genome ? AF: 0.00575 AC: 875AN: 152186Hom.: 4 Cov.: 32 AF XY: 0.00611 AC XY: 455AN XY: 74408
ClinVar
Submissions by phenotype
Dystonia 24 Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Jun 28, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 01, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | ANO3: BP4, BP7, BS2 - |
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at