5-131430969-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016340.6(RAPGEF6):āc.4355A>Gā(p.Gln1452Arg) variant causes a missense change. The variant allele was found at a frequency of 0.851 in 1,614,014 control chromosomes in the GnomAD database, including 585,619 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_016340.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAPGEF6 | NM_016340.6 | c.4355A>G | p.Gln1452Arg | missense_variant | 26/28 | ENST00000509018.6 | NP_057424.3 | |
RAPGEF6 | NM_001164386.2 | c.4379A>G | p.Gln1460Arg | missense_variant | 27/29 | NP_001157858.1 | ||
RAPGEF6 | NM_001164387.2 | c.4394A>G | p.Gln1465Arg | missense_variant | 28/29 | NP_001157859.1 | ||
RAPGEF6 | NM_001164388.2 | c.4379A>G | p.Gln1460Arg | missense_variant | 27/28 | NP_001157860.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAPGEF6 | ENST00000509018.6 | c.4355A>G | p.Gln1452Arg | missense_variant | 26/28 | 1 | NM_016340.6 | ENSP00000421684.1 | ||
ENSG00000273217 | ENST00000514667.1 | c.4505A>G | p.Gln1502Arg | missense_variant | 27/29 | 2 | ENSP00000426948.1 |
Frequencies
GnomAD3 genomes AF: 0.879 AC: 133683AN: 152076Hom.: 59027 Cov.: 31
GnomAD3 exomes AF: 0.861 AC: 216554AN: 251422Hom.: 93478 AF XY: 0.857 AC XY: 116447AN XY: 135876
GnomAD4 exome AF: 0.848 AC: 1240178AN: 1461820Hom.: 526530 Cov.: 66 AF XY: 0.848 AC XY: 616505AN XY: 727208
GnomAD4 genome AF: 0.879 AC: 133803AN: 152194Hom.: 59089 Cov.: 31 AF XY: 0.878 AC XY: 65358AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at