rs56110425
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001353921.2(ARHGEF9):c.1225A>G(p.Ile409Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,209,578 control chromosomes in the GnomAD database, including 1 homozygotes. There are 49 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001353921.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF9 | NM_001353921.2 | c.1225A>G | p.Ile409Val | missense_variant | Exon 8 of 10 | ENST00000671741.2 | NP_001340850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF9 | ENST00000671741.2 | c.1225A>G | p.Ile409Val | missense_variant | Exon 8 of 10 | NM_001353921.2 | ENSP00000500715.1 |
Frequencies
GnomAD3 genomes AF: 0.000179 AC: 20AN: 111732Hom.: 1 Cov.: 22 AF XY: 0.0000590 AC XY: 2AN XY: 33912
GnomAD3 exomes AF: 0.000296 AC: 54AN: 182738Hom.: 0 AF XY: 0.000237 AC XY: 16AN XY: 67484
GnomAD4 exome AF: 0.000146 AC: 160AN: 1097846Hom.: 0 Cov.: 31 AF XY: 0.000129 AC XY: 47AN XY: 363372
GnomAD4 genome AF: 0.000179 AC: 20AN: 111732Hom.: 1 Cov.: 22 AF XY: 0.0000590 AC XY: 2AN XY: 33912
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 8 Benign:2
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ARHGEF9-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
ARHGEF9: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at