9-129095489-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000755.5(CRAT):c.1789G>A(p.Glu597Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000755.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRAT | NM_000755.5 | c.1789G>A | p.Glu597Lys | missense_variant | Exon 14 of 14 | ENST00000318080.7 | NP_000746.3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250124Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135654
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461168Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726902
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1789G>A (p.E597K) alteration is located in exon 14 (coding exon 14) of the CRAT gene. This alteration results from a G to A substitution at nucleotide position 1789, causing the glutamic acid (E) at amino acid position 597 to be replaced by a lysine (K). 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