11-65321163-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006779.4(CDC42EP2):c.265G>A(p.Ala89Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006779.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDC42EP2 | NM_006779.4 | c.265G>A | p.Ala89Thr | missense_variant | 2/2 | ENST00000279249.3 | NP_006770.1 | |
CDC42EP2 | XM_047426244.1 | c.265G>A | p.Ala89Thr | missense_variant | 2/2 | XP_047282200.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC42EP2 | ENST00000279249.3 | c.265G>A | p.Ala89Thr | missense_variant | 2/2 | 1 | NM_006779.4 | ENSP00000279249.2 | ||
ENSG00000285816 | ENST00000649896.1 | n.*591G>A | non_coding_transcript_exon_variant | 19/20 | ENSP00000498025.1 | |||||
ENSG00000285816 | ENST00000649896.1 | n.*591G>A | 3_prime_UTR_variant | 19/20 | ENSP00000498025.1 | |||||
CDC42EP2 | ENST00000533419.1 | c.265G>A | p.Ala89Thr | missense_variant | 2/2 | 3 | ENSP00000431660.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251150Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135784
GnomAD4 exome AF: 0.000120 AC: 176AN: 1461804Hom.: 0 Cov.: 32 AF XY: 0.000114 AC XY: 83AN XY: 727194
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.265G>A (p.A89T) alteration is located in exon 2 (coding exon 1) of the CDC42EP2 gene. This alteration results from a G to A substitution at nucleotide position 265, causing the alanine (A) at amino acid position 89 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