6-16327184-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001128164.2(ATXN1):c.1127C>T(p.Ser376Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN1 | NM_001128164.2 | c.1127C>T | p.Ser376Leu | missense_variant | Exon 7 of 8 | ENST00000436367.6 | NP_001121636.1 | |
ATXN1 | NM_000332.4 | c.1127C>T | p.Ser376Leu | missense_variant | Exon 8 of 9 | NP_000323.2 | ||
ATXN1 | NM_001357857.2 | c.*540C>T | 3_prime_UTR_variant | Exon 8 of 9 | NP_001344786.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN1 | ENST00000436367.6 | c.1127C>T | p.Ser376Leu | missense_variant | Exon 7 of 8 | 1 | NM_001128164.2 | ENSP00000416360.1 | ||
ATXN1 | ENST00000244769.8 | c.1127C>T | p.Ser376Leu | missense_variant | Exon 8 of 9 | 1 | ENSP00000244769.3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251054Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135736
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461594Hom.: 0 Cov.: 99 AF XY: 0.0000193 AC XY: 14AN XY: 727110
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1127C>T (p.S376L) alteration is located in exon 8 (coding exon 1) of the ATXN1 gene. This alteration results from a C to T substitution at nucleotide position 1127, causing the serine (S) at amino acid position 376 to be replaced by a leucine (L). 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