3-44243486-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145030.2(TOPAZ1):c.980G>A(p.Gly327Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,551,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145030.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOPAZ1 | NM_001145030.2 | c.980G>A | p.Gly327Glu | missense_variant | 2/20 | ENST00000309765.4 | |
TOPAZ1 | XM_011533694.3 | c.980G>A | p.Gly327Glu | missense_variant | 2/20 | ||
TOPAZ1 | XM_017006361.2 | c.980G>A | p.Gly327Glu | missense_variant | 2/18 | ||
TOPAZ1 | XM_017006362.1 | c.980G>A | p.Gly327Glu | missense_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOPAZ1 | ENST00000309765.4 | c.980G>A | p.Gly327Glu | missense_variant | 2/20 | 5 | NM_001145030.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1399426Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 690204
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2022 | The c.980G>A (p.G327E) alteration is located in exon 2 (coding exon 2) of the TOPAZ1 gene. This alteration results from a G to A substitution at nucleotide position 980, causing the glycine (G) at amino acid position 327 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