10-118754576-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153810.5(CACUL1):c.187G>A(p.Val63Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000415 in 1,609,760 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_153810.5 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 |
---|---|---|---|---|---|---|---|---|---|---|
CACUL1 | ENST00000369151.8 | c.187G>A | p.Val63Ile | missense_variant | Exon 1 of 9 | 1 | NM_153810.5 | ENSP00000358147.2 | ||
CACUL1 | ENST00000493518.5 | n.187G>A | non_coding_transcript_exon_variant | Exon 1 of 10 | 1 | ENSP00000431329.1 | ||||
CACUL1 | ENST00000477583.1 | n.-99G>A | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000130 AC: 30AN: 231442Hom.: 0 AF XY: 0.000118 AC XY: 15AN XY: 127408
GnomAD4 exome AF: 0.000433 AC: 631AN: 1457452Hom.: 0 Cov.: 32 AF XY: 0.000422 AC XY: 306AN XY: 725044
GnomAD4 genome AF: 0.000243 AC: 37AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.187G>A (p.V63I) alteration is located in exon 1 (coding exon 1) of the CACUL1 gene. This alteration results from a G to A substitution at nucleotide position 187, causing the valine (V) at amino acid position 63 to be replaced by an isoleucine (I). 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