6-16306357-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001128164.2(ATXN1):c.2420T>C(p.Ile807Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,459,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN1 | NM_001128164.2 | c.2420T>C | p.Ile807Thr | missense_variant | Exon 8 of 8 | ENST00000436367.6 | NP_001121636.1 | |
ATXN1 | NM_000332.4 | c.2420T>C | p.Ile807Thr | missense_variant | Exon 9 of 9 | NP_000323.2 | ||
ATXN1 | NM_001357857.2 | c.*1833T>C | 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.2420T>C | p.Ile807Thr | missense_variant | Exon 8 of 8 | 1 | NM_001128164.2 | ENSP00000416360.1 | ||
ATXN1 | ENST00000244769.8 | c.2420T>C | p.Ile807Thr | missense_variant | Exon 9 of 9 | 1 | ENSP00000244769.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250608Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135522
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1459996Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726206
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2420T>C (p.I807T) alteration is located in exon 9 (coding exon 2) of the ATXN1 gene. This alteration results from a T to C substitution at nucleotide position 2420, causing the isoleucine (I) at amino acid position 807 to be replaced by a threonine (T). 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