chr12-47744064-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001098531.4(RAPGEF3):c.1601G>A(p.Arg534Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000312 in 1,601,500 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_001098531.4 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 | UniProt |
---|---|---|---|---|---|---|---|
RAPGEF3 | NM_001098531.4 | c.1601G>A | p.Arg534Gln | missense_variant | 17/28 | ENST00000449771.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPGEF3 | ENST00000449771.7 | c.1601G>A | p.Arg534Gln | missense_variant | 17/28 | 2 | NM_001098531.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000564 AC: 14AN: 248378Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134578
GnomAD4 exome AF: 0.0000311 AC: 45AN: 1449242Hom.: 0 Cov.: 31 AF XY: 0.0000263 AC XY: 19AN XY: 721770
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1601G>A (p.R534Q) alteration is located in exon 17 (coding exon 17) of the RAPGEF3 gene. This alteration results from a G to A substitution at nucleotide position 1601, causing the arginine (R) at amino acid position 534 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