17-44195475-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001382309.1(ATXN7L3):āc.565A>Gā(p.Thr189Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001382309.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN7L3 | NM_001382309.1 | c.565A>G | p.Thr189Ala | missense_variant | 9/13 | ENST00000587097.6 | NP_001369238.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249462Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135364
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727194
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.586A>G (p.T196A) alteration is located in exon 8 (coding exon 8) of the ATXN7L3 gene. This alteration results from a A to G substitution at nucleotide position 586, causing the threonine (T) at amino acid position 196 to be replaced by an alanine (A). 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