9-131602095-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001377935.1(RAPGEF1):c.2467G>A(p.Val823Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000617 in 1,604,222 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_001377935.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAPGEF1 | NM_001377935.1 | c.2467G>A | p.Val823Ile | missense_variant | 15/27 | ENST00000683357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPGEF1 | ENST00000683357.1 | c.2467G>A | p.Val823Ile | missense_variant | 15/27 | NM_001377935.1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000863 AC: 20AN: 231818Hom.: 0 AF XY: 0.0000953 AC XY: 12AN XY: 125940
GnomAD4 exome AF: 0.0000510 AC: 74AN: 1452096Hom.: 0 Cov.: 31 AF XY: 0.0000554 AC XY: 40AN XY: 721474
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.1963G>A (p.V655I) alteration is located in exon 12 (coding exon 12) of the RAPGEF1 gene. This alteration results from a G to A substitution at nucleotide position 1963, causing the valine (V) at amino acid position 655 to be replaced by an isoleucine (I). 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