22-30285645-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001037666.3(CASTOR1):c.965G>A(p.Arg322Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000433 in 1,570,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001037666.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASTOR1 | ENST00000407689.8 | c.965G>A | p.Arg322Gln | missense_variant | Exon 9 of 9 | 1 | NM_001037666.3 | ENSP00000384183.4 | ||
ENSG00000248751 | ENST00000434291.5 | c.1418G>A | p.Arg473Gln | missense_variant | Exon 13 of 13 | 2 | ENSP00000401535.1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152198Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000105 AC: 19AN: 181320Hom.: 0 AF XY: 0.000112 AC XY: 11AN XY: 98452
GnomAD4 exome AF: 0.0000261 AC: 37AN: 1417862Hom.: 0 Cov.: 31 AF XY: 0.0000228 AC XY: 16AN XY: 701726
GnomAD4 genome AF: 0.000204 AC: 31AN: 152316Hom.: 0 Cov.: 34 AF XY: 0.000201 AC XY: 15AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.965G>A (p.R322Q) alteration is located in exon 9 (coding exon 9) of the GATSL3 gene. This alteration results from a G to A substitution at nucleotide position 965, causing the arginine (R) at amino acid position 322 to be replaced by a glutamine (Q). 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