chr12-93678817-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003805.5(CRADD):c.43G>A(p.Glu15Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. E15D) has been classified as Likely benign.
Frequency
Consequence
NM_003805.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRADD | NM_003805.5 | c.43G>A | p.Glu15Lys | missense_variant | 2/3 | ENST00000332896.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRADD | ENST00000332896.8 | c.43G>A | p.Glu15Lys | missense_variant | 2/3 | 1 | NM_003805.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250908Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135702
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727212
GnomAD4 genome AF: 0.000131 AC: 20AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74498
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 15 of the CRADD protein (p.Glu15Lys). This variant is present in population databases (rs150059138, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with CRADD-related conditions. ClinVar contains an entry for this variant (Variation ID: 2192965). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at