22-30285679-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.931G>A(p.Asp311Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000268 in 1,566,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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.931G>A | p.Asp311Asn | missense_variant | Exon 9 of 9 | 1 | NM_001037666.3 | ENSP00000384183.4 | ||
ENSG00000248751 | ENST00000434291.5 | c.1384G>A | p.Asp462Asn | missense_variant | Exon 13 of 13 | 2 | ENSP00000401535.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000212 AC: 37AN: 174656Hom.: 0 AF XY: 0.000181 AC XY: 17AN XY: 94090
GnomAD4 exome AF: 0.0000290 AC: 41AN: 1414400Hom.: 0 Cov.: 31 AF XY: 0.0000272 AC XY: 19AN XY: 699304
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.931G>A (p.D311N) 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 931, causing the aspartic acid (D) at amino acid position 311 to be replaced by an asparagine (N). 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