X-13318940-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001135995.2(ATXN3L):c.995G>A(p.Gly332Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,208,315 control chromosomes in the GnomAD database, including 76,102 homozygotes. There are 160,490 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001135995.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATXN3L | NM_001135995.2 | c.995G>A | p.Gly332Asp | missense_variant | 1/1 | ENST00000380622.5 | NP_001129467.1 | |
ATXN3L | NM_001387036.1 | c.731G>A | p.Gly244Asp | missense_variant | 2/2 | NP_001373965.1 | ||
GS1-600G8.3 | NR_046087.1 | n.1449-68C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATXN3L | ENST00000380622.5 | c.995G>A | p.Gly332Asp | missense_variant | 1/1 | 6 | NM_001135995.2 | ENSP00000369996.2 | ||
GS1-600G8.3 | ENST00000431486.1 | n.1449-68C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.508 AC: 56172AN: 110634Hom.: 11751 Cov.: 23 AF XY: 0.508 AC XY: 16677AN XY: 32852
GnomAD3 exomes AF: 0.495 AC: 89477AN: 180865Hom.: 17332 AF XY: 0.471 AC XY: 31697AN XY: 67283
GnomAD4 exome AF: 0.395 AC: 433297AN: 1097631Hom.: 64333 Cov.: 34 AF XY: 0.396 AC XY: 143756AN XY: 363233
GnomAD4 genome AF: 0.508 AC: 56244AN: 110684Hom.: 11769 Cov.: 23 AF XY: 0.508 AC XY: 16734AN XY: 32912
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at