rs41267702
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001128164.2(ATXN1):c.2150C>T(p.Ala717Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00431 in 1,614,222 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001128164.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN1 | NM_001128164.2 | c.2150C>T | p.Ala717Val | missense_variant | 8/8 | ENST00000436367.6 | |
ATXN1 | NM_000332.4 | c.2150C>T | p.Ala717Val | missense_variant | 9/9 | ||
ATXN1 | NM_001357857.2 | c.*1563C>T | 3_prime_UTR_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN1 | ENST00000436367.6 | c.2150C>T | p.Ala717Val | missense_variant | 8/8 | 1 | NM_001128164.2 | P1 | |
ATXN1 | ENST00000244769.8 | c.2150C>T | p.Ala717Val | missense_variant | 9/9 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00285 AC: 434AN: 152214Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00274 AC: 688AN: 251400Hom.: 0 AF XY: 0.00285 AC XY: 387AN XY: 135870
GnomAD4 exome AF: 0.00446 AC: 6526AN: 1461890Hom.: 25 Cov.: 31 AF XY: 0.00436 AC XY: 3170AN XY: 727244
GnomAD4 genome ? AF: 0.00285 AC: 434AN: 152332Hom.: 3 Cov.: 33 AF XY: 0.00262 AC XY: 195AN XY: 74494
ClinVar
Submissions by phenotype
Spinocerebellar ataxia type 1 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Jul 28, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Jul 31, 2017 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital | Oct 30, 2017 | BS1, BP4; This alteration has an allele frequency that is greater than expected for the associated disease, and is predicted to be tolerated by multiple functional prediction tools. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at