rs112463375
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_173728.4(ARHGEF15):c.2463G>C(p.Gln821His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000243 in 1,614,014 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_173728.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF15 | NM_173728.4 | c.2463G>C | p.Gln821His | missense_variant | 16/16 | ENST00000361926.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF15 | ENST00000361926.8 | c.2463G>C | p.Gln821His | missense_variant | 16/16 | 1 | NM_173728.4 | P1 | |
ARHGEF15 | ENST00000421050.2 | c.2463G>C | p.Gln821His | missense_variant | 16/16 | 1 | P1 | ||
ARHGEF15 | ENST00000647883.1 | c.1926G>C | p.Gln642His | missense_variant | 13/13 |
Frequencies
GnomAD3 genomes ? AF: 0.00106 AC: 162AN: 152158Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000278 AC: 70AN: 251464Hom.: 1 AF XY: 0.000228 AC XY: 31AN XY: 135920
GnomAD4 exome AF: 0.000157 AC: 229AN: 1461738Hom.: 2 Cov.: 53 AF XY: 0.000144 AC XY: 105AN XY: 727166
GnomAD4 genome ? AF: 0.00107 AC: 163AN: 152276Hom.: 1 Cov.: 31 AF XY: 0.000940 AC XY: 70AN XY: 74436
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at