NM_001128164.2:c.1924G>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001128164.2(ATXN1):c.1924G>A(p.Val642Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000483 in 1,450,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001128164.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN1 | NM_001128164.2 | c.1924G>A | p.Val642Ile | missense_variant | Exon 8 of 8 | ENST00000436367.6 | NP_001121636.1 | |
ATXN1 | NM_000332.4 | c.1924G>A | p.Val642Ile | missense_variant | Exon 9 of 9 | NP_000323.2 | ||
ATXN1 | NM_001357857.2 | c.*1337G>A | 3_prime_UTR_variant | Exon 9 of 9 | NP_001344786.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN1 | ENST00000436367.6 | c.1924G>A | p.Val642Ile | missense_variant | Exon 8 of 8 | 1 | NM_001128164.2 | ENSP00000416360.1 | ||
ATXN1 | ENST00000244769.8 | c.1924G>A | p.Val642Ile | missense_variant | Exon 9 of 9 | 1 | ENSP00000244769.3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152192Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 exomes AF: 0.0000208 AC: 5AN: 240172Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130830
GnomAD4 exome AF: 0.00000483 AC: 7AN: 1450360Hom.: 0 Cov.: 31 AF XY: 0.00000416 AC XY: 3AN XY: 721354
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74352
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1924G>A (p.V642I) alteration is located in exon 9 (coding exon 2) of the ATXN1 gene. This alteration results from a G to A substitution at nucleotide position 1924, causing the valine (V) at amino acid position 642 to be replaced by an isoleucine (I). 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