chr9-131584333-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_001377935.1(RAPGEF1):c.3392A>G(p.Glu1131Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,612,436 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. E1131A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001377935.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAPGEF1 | NM_001377935.1 | c.3392A>G | p.Glu1131Gly | missense_variant | 24/27 | ENST00000683357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPGEF1 | ENST00000683357.1 | c.3392A>G | p.Glu1131Gly | missense_variant | 24/27 | NM_001377935.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000978 AC: 24AN: 245488Hom.: 0 AF XY: 0.0000900 AC XY: 12AN XY: 133384
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1460370Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726400
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | The c.2888A>G (p.E963G) alteration is located in exon 21 (coding exon 21) of the RAPGEF1 gene. This alteration results from a A to G substitution at nucleotide position 2888, causing the glutamic acid (E) at amino acid position 963 to be replaced by a glycine (G). 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