17-79834258-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003655.3(CBX4):c.1384G>A(p.Val462Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 1,605,108 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_003655.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBX4 | NM_003655.3 | c.1384G>A | p.Val462Ile | missense_variant | Exon 5 of 5 | ENST00000269397.9 | NP_003646.2 | |
CBX4 | XM_011525399.3 | c.1186G>A | p.Val396Ile | missense_variant | Exon 3 of 3 | XP_011523701.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000132 AC: 3AN: 226744Hom.: 0 AF XY: 0.0000239 AC XY: 3AN XY: 125642
GnomAD4 exome AF: 0.00000551 AC: 8AN: 1452956Hom.: 0 Cov.: 32 AF XY: 0.00000554 AC XY: 4AN XY: 722202
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1384G>A (p.V462I) alteration is located in exon 5 (coding exon 5) of the CBX4 gene. This alteration results from a G to A substitution at nucleotide position 1384, causing the valine (V) at amino acid position 462 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