chr12-47743658-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001098531.4(RAPGEF3):c.1697G>A(p.Arg566Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000249 in 1,609,470 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 (★).
Frequency
Consequence
NM_001098531.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAPGEF3 | NM_001098531.4 | c.1697G>A | p.Arg566Gln | missense_variant | 18/28 | ENST00000449771.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPGEF3 | ENST00000449771.7 | c.1697G>A | p.Arg566Gln | missense_variant | 18/28 | 2 | NM_001098531.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000144 AC: 36AN: 250546Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135392
GnomAD4 exome AF: 0.000263 AC: 383AN: 1457336Hom.: 0 Cov.: 31 AF XY: 0.000251 AC XY: 182AN XY: 723874
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152134Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.1697G>A (p.R566Q) alteration is located in exon 18 (coding exon 18) of the RAPGEF3 gene. This alteration results from a G to A substitution at nucleotide position 1697, causing the arginine (R) at amino acid position 566 to be replaced by a glutamine (Q). 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