16-71850180-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001137675.4(ATXN1L):c.440C>A(p.Pro147His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000825 in 1,551,604 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_001137675.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN1L | ENST00000427980.7 | c.440C>A | p.Pro147His | missense_variant | Exon 3 of 3 | 1 | NM_001137675.4 | ENSP00000415822.2 | ||
ATXN1L | ENST00000683775.1 | c.440C>A | p.Pro147His | missense_variant | Exon 3 of 3 | ENSP00000507897.1 | ||||
IST1 | ENST00000568581.5 | c.-16+2109C>A | intron_variant | Intron 2 of 4 | 5 | ENSP00000456200.1 | ||||
ATXN1L | ENST00000569119.1 | n.119+2109C>A | intron_variant | Intron 2 of 3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000713 AC: 11AN: 154234Hom.: 0 AF XY: 0.0000367 AC XY: 3AN XY: 81800
GnomAD4 exome AF: 0.0000829 AC: 116AN: 1399448Hom.: 0 Cov.: 30 AF XY: 0.0000855 AC XY: 59AN XY: 690224
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.440C>A (p.P147H) alteration is located in exon 3 (coding exon 1) of the ATXN1L gene. This alteration results from a C to A substitution at nucleotide position 440, causing the proline (P) at amino acid position 147 to be replaced by a histidine (H). 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