rs542401270
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004993.6(ATXN3):c.1000A>G(p.Met334Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,609,156 control chromosomes in the GnomAD database, including 2 homozygotes. 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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000529 AC: 131AN: 247742Hom.: 1 AF XY: 0.000664 AC XY: 89AN XY: 134042
GnomAD4 exome AF: 0.000238 AC: 346AN: 1456798Hom.: 2 Cov.: 29 AF XY: 0.000333 AC XY: 241AN XY: 724566
GnomAD4 genome AF: 0.000203 AC: 31AN: 152358Hom.: 0 Cov.: 32 AF XY: 0.000322 AC XY: 24AN XY: 74510
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1000A>G (p.M334V) alteration is located in exon 11 (coding exon 11) of the ATXN3 gene. This alteration results from a A to G substitution at nucleotide position 1000, causing the methionine (M) at amino acid position 334 to be replaced by a valine (V). 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