chr14-92070979-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004993.6(ATXN3):c.947G>A(p.Cys316Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000728 in 1,236,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004993.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN3 | NM_004993.6 | c.947G>A | p.Cys316Tyr | missense_variant | 10/11 | ENST00000644486.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN3 | ENST00000644486.2 | c.947G>A | p.Cys316Tyr | missense_variant | 10/11 | NM_004993.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000941 AC: 5AN: 53110Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.00000503 AC: 1AN: 198912Hom.: 0 AF XY: 0.00000910 AC XY: 1AN XY: 109878
GnomAD4 exome AF: 0.00000338 AC: 4AN: 1183022Hom.: 0 Cov.: 80 AF XY: 0.00000345 AC XY: 2AN XY: 580468
GnomAD4 genome ? AF: 0.0000941 AC: 5AN: 53110Hom.: 0 Cov.: 0 AF XY: 0.000154 AC XY: 4AN XY: 26014
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2022 | The c.947G>A (p.C316Y) alteration is located in exon 10 (coding exon 10) of the ATXN3 gene. This alteration results from a G to A substitution at nucleotide position 947, causing the cysteine (C) at amino acid position 316 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at