1-109490061-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001350175.2(ATXN7L2):c.1265G>A(p.Gly422Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000429 in 1,607,378 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001350175.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN7L2 | NM_001350175.2 | c.1265G>A | p.Gly422Glu | missense_variant | 8/11 | ENST00000683729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN7L2 | ENST00000683729.1 | c.1265G>A | p.Gly422Glu | missense_variant | 8/11 | NM_001350175.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000413 AC: 10AN: 242086Hom.: 0 AF XY: 0.0000534 AC XY: 7AN XY: 131172
GnomAD4 exome AF: 0.0000419 AC: 61AN: 1455206Hom.: 0 Cov.: 31 AF XY: 0.0000415 AC XY: 30AN XY: 723680
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.1169G>A (p.G390E) alteration is located in exon 8 (coding exon 8) of the ATXN7L2 gene. This alteration results from a G to A substitution at nucleotide position 1169, causing the glycine (G) at amino acid position 390 to be replaced by a glutamic acid (E). 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