rs56182751
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001353921.2(ARHGEF9):c.579G>A(p.Glu193Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000406 in 1,207,168 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001353921.2 synonymous
Scores
Clinical Significance
Conservation
Publications
- developmental and epileptic encephalopathy, 8Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet
- X-linked complex neurodevelopmental disorderInheritance: XL Classification: MODERATE Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF9 | NM_001353921.2 | c.579G>A | p.Glu193Glu | synonymous_variant | Exon 4 of 10 | ENST00000671741.2 | NP_001340850.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF9 | ENST00000671741.2 | c.579G>A | p.Glu193Glu | synonymous_variant | Exon 4 of 10 | NM_001353921.2 | ENSP00000500715.1 |
Frequencies
GnomAD3 genomes AF: 0.000153 AC: 17AN: 111389Hom.: 0 Cov.: 22 show subpopulations
GnomAD2 exomes AF: 0.0000283 AC: 5AN: 176647 AF XY: 0.0000161 show subpopulations
GnomAD4 exome AF: 0.0000292 AC: 32AN: 1095779Hom.: 0 Cov.: 30 AF XY: 0.0000304 AC XY: 11AN XY: 361683 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000153 AC: 17AN: 111389Hom.: 0 Cov.: 22 AF XY: 0.0000595 AC XY: 2AN XY: 33597 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:2
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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). -
Developmental and epileptic encephalopathy, 8 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at