chr12-111214215-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_015267.4(CUX2):c.79G>A(p.Val27Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,496,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V27F) has been classified as Likely benign.
Frequency
Consequence
NM_015267.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUX2 | NM_015267.4 | c.79G>A | p.Val27Ile | missense_variant | 2/22 | ENST00000261726.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUX2 | ENST00000261726.11 | c.79G>A | p.Val27Ile | missense_variant | 2/22 | 1 | NM_015267.4 | P1 | |
CUX2 | ENST00000397643.3 | c.259G>A | p.Val87Ile | missense_variant | 3/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000147 AC: 2AN: 136194Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000989 AC: 2AN: 202220Hom.: 0 AF XY: 0.00000899 AC XY: 1AN XY: 111174
GnomAD4 exome AF: 0.0000272 AC: 37AN: 1360578Hom.: 0 Cov.: 28 AF XY: 0.0000296 AC XY: 20AN XY: 674578
GnomAD4 genome ? AF: 0.0000147 AC: 2AN: 136194Hom.: 0 Cov.: 30 AF XY: 0.0000154 AC XY: 1AN XY: 64932
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 29, 2021 | The c.79G>A (p.V27I) alteration is located in exon 2 (coding exon 2) of the CUX2 gene. This alteration results from a G to A substitution at nucleotide position 79, causing the valine (V) at amino acid position 27 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