chr9-131621846-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001377935.1(RAPGEF1):c.1855G>A(p.Val619Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,611,340 control chromosomes in the GnomAD database, including 1 homozygotes. 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.1855G>A | p.Val619Met | missense_variant | 11/27 | ENST00000683357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPGEF1 | ENST00000683357.1 | c.1855G>A | p.Val619Met | missense_variant | 11/27 | NM_001377935.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000371 AC: 9AN: 242880Hom.: 0 AF XY: 0.0000379 AC XY: 5AN XY: 131948
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459060Hom.: 1 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 725550
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.1858G>A (p.V620M) alteration is located in exon 11 (coding exon 11) of the RAPGEF1 gene. This alteration results from a G to A substitution at nucleotide position 1858, causing the valine (V) at amino acid position 620 to be replaced by a methionine (M). 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