chr11-64829654-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017525.3(CDC42BPG):c.3784G>A(p.Ala1262Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017525.3 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 |
---|---|---|---|---|---|---|---|
CDC42BPG | NM_017525.3 | c.3784G>A | p.Ala1262Thr | missense_variant | 30/37 | ENST00000342711.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC42BPG | ENST00000342711.6 | c.3784G>A | p.Ala1262Thr | missense_variant | 30/37 | 1 | NM_017525.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000417 AC: 1AN: 239732Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131420
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459092Hom.: 0 Cov.: 76 AF XY: 0.00 AC XY: 0AN XY: 725808
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.3784G>A (p.A1262T) alteration is located in exon 30 (coding exon 30) of the CDC42BPG gene. This alteration results from a G to A substitution at nucleotide position 3784, causing the alanine (A) at amino acid position 1262 to be replaced by a threonine (T). 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