rs3802751
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_031418.4(ANO3):c.977-6T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00571 in 1,610,656 control chromosomes in the GnomAD database, including 311 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_031418.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO3 | NM_031418.4 | c.977-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000256737.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO3 | ENST00000256737.8 | c.977-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_031418.4 | P3 | |||
ANO3 | ENST00000525139.5 | c.929-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
ANO3 | ENST00000531568.1 | c.539-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | A1 | ||||
ANO3 | ENST00000672621.1 | c.1160-6T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00785 AC: 1194AN: 152196Hom.: 30 Cov.: 32
GnomAD3 exomes AF: 0.0116 AC: 2914AN: 251374Hom.: 62 AF XY: 0.0103 AC XY: 1405AN XY: 135860
GnomAD4 exome AF: 0.00549 AC: 8004AN: 1458342Hom.: 281 Cov.: 29 AF XY: 0.00536 AC XY: 3892AN XY: 725758
GnomAD4 genome ? AF: 0.00785 AC: 1196AN: 152314Hom.: 30 Cov.: 32 AF XY: 0.0106 AC XY: 793AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2018 | - - |
Dystonia 24 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Dystonic disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at