17-8319552-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_173728.4(ARHGEF15):c.2323C>T(p.Arg775Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 1,611,294 control chromosomes in the GnomAD database, including 694 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R775Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_173728.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF15 | NM_173728.4 | c.2323C>T | p.Arg775Trp | missense_variant | 15/16 | ENST00000361926.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF15 | ENST00000361926.8 | c.2323C>T | p.Arg775Trp | missense_variant | 15/16 | 1 | NM_173728.4 | P1 | |
ARHGEF15 | ENST00000421050.2 | c.2323C>T | p.Arg775Trp | missense_variant | 15/16 | 1 | P1 | ||
ARHGEF15 | ENST00000647883.1 | c.1786C>T | p.Arg596Trp | missense_variant | 12/13 |
Frequencies
GnomAD3 genomes AF: 0.0224 AC: 3402AN: 152196Hom.: 49 Cov.: 32
GnomAD3 exomes AF: 0.0234 AC: 5816AN: 248436Hom.: 108 AF XY: 0.0255 AC XY: 3430AN XY: 134286
GnomAD4 exome AF: 0.0267 AC: 39010AN: 1458980Hom.: 645 Cov.: 32 AF XY: 0.0275 AC XY: 19990AN XY: 725794
GnomAD4 genome AF: 0.0223 AC: 3403AN: 152314Hom.: 49 Cov.: 32 AF XY: 0.0215 AC XY: 1605AN XY: 74484
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at