chr17-8315267-G-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_173728.4(ARHGEF15):c.1250G>T(p.Arg417Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0025 in 1,612,902 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts 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 Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF15 | NM_173728.4 | c.1250G>T | p.Arg417Leu | missense_variant | Exon 6 of 16 | ENST00000361926.8 | NP_776089.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF15 | ENST00000361926.8 | c.1250G>T | p.Arg417Leu | missense_variant | Exon 6 of 16 | 1 | NM_173728.4 | ENSP00000355026.3 | ||
ARHGEF15 | ENST00000421050.2 | c.1250G>T | p.Arg417Leu | missense_variant | Exon 6 of 16 | 1 | ENSP00000412505.1 | |||
ARHGEF15 | ENST00000647883.1 | c.713G>T | p.Arg238Leu | missense_variant | Exon 3 of 13 | ENSP00000498197.1 | ||||
ARHGEF15 | ENST00000578286.1 | n.298G>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00249 AC: 378AN: 152070Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00254 AC: 630AN: 248104Hom.: 2 AF XY: 0.00244 AC XY: 328AN XY: 134674
GnomAD4 exome AF: 0.00250 AC: 3654AN: 1460714Hom.: 14 Cov.: 33 AF XY: 0.00256 AC XY: 1863AN XY: 726668
GnomAD4 genome AF: 0.00248 AC: 378AN: 152188Hom.: 2 Cov.: 31 AF XY: 0.00241 AC XY: 179AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:2
- -
ARHGEF15: BP4, BS2 -
Early infantile epileptic encephalopathy with suppression bursts Benign:1
- -
See cases Benign:1
This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at