chr17-8312106-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_173728.4(ARHGEF15):c.67C>T(p.Arg23Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,581,580 control chromosomes in the GnomAD database, including 310 homozygotes. In-silico tool predicts 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. R23H) 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF15 | NM_173728.4 | c.67C>T | p.Arg23Cys | missense_variant | 2/16 | ENST00000361926.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF15 | ENST00000361926.8 | c.67C>T | p.Arg23Cys | missense_variant | 2/16 | 1 | NM_173728.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00778 AC: 1161AN: 149206Hom.: 48 Cov.: 22
GnomAD3 exomes AF: 0.0134 AC: 3042AN: 227000Hom.: 202 AF XY: 0.00985 AC XY: 1208AN XY: 122650
GnomAD4 exome AF: 0.00291 AC: 4161AN: 1432260Hom.: 263 Cov.: 36 AF XY: 0.00245 AC XY: 1747AN XY: 711924
GnomAD4 genome ? AF: 0.00778 AC: 1162AN: 149320Hom.: 47 Cov.: 22 AF XY: 0.00908 AC XY: 661AN XY: 72812
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
ARHGEF15-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 13, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at