7-105614608-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020725.2(ATXN7L1):c.1726G>A(p.Ala576Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000529 in 1,551,446 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_020725.2 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 |
---|---|---|---|---|---|---|---|---|
ATXN7L1 | NM_020725.2 | c.1726G>A | p.Ala576Thr | missense_variant | Exon 10 of 12 | ENST00000419735.8 | NP_065776.1 | |
ATXN7L1 | NM_001385596.1 | c.1726G>A | p.Ala576Thr | missense_variant | Exon 10 of 12 | NP_001372525.1 | ||
ATXN7L1 | NM_138495.2 | c.1354G>A | p.Ala452Thr | missense_variant | Exon 8 of 10 | NP_612504.1 | ||
ATXN7L1 | NM_001318229.2 | c.1078G>A | p.Ala360Thr | missense_variant | Exon 10 of 10 | NP_001305158.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000987 AC: 15AN: 151938Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000765 AC: 12AN: 156954Hom.: 0 AF XY: 0.000108 AC XY: 9AN XY: 83066
GnomAD4 exome AF: 0.0000479 AC: 67AN: 1399508Hom.: 0 Cov.: 32 AF XY: 0.0000608 AC XY: 42AN XY: 690266
GnomAD4 genome AF: 0.0000987 AC: 15AN: 151938Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74176
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1726G>A (p.A576T) alteration is located in exon 10 (coding exon 10) of the ATXN7L1 gene. This alteration results from a G to A substitution at nucleotide position 1726, causing the alanine (A) at amino acid position 576 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