rs145204305
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_173728.4(ARHGEF15):c.2388G>T(p.Gly796=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000528 in 1,612,684 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00028 ( 2 hom. )
Consequence
ARHGEF15
NM_173728.4 synonymous
NM_173728.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.326
Genes affected
ARHGEF15 (HGNC:15590): (Rho guanine nucleotide exchange factor 15) Rho GTPases play a fundamental role in numerous cellular processes that are initiated by extracellular stimuli that work through G protein-coupled receptors. This gene encodes a protein that functions as a specific guanine nucleotide exchange factor for RhoA. It also interacts with ephrin A4 in vascular smooth muscle cells. Two alternatively spliced transcripts variants that encode the same protein have been found for this gene. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 17-8320855-G-T is Benign according to our data. Variant chr17-8320855-G-T is described in ClinVar as [Benign]. Clinvar id is 461433.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.326 with no splicing effect.
BS2
?
High Homozygotes in GnomAd4 at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGEF15 | NM_173728.4 | c.2388G>T | p.Gly796= | synonymous_variant | 16/16 | ENST00000361926.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGEF15 | ENST00000361926.8 | c.2388G>T | p.Gly796= | synonymous_variant | 16/16 | 1 | NM_173728.4 | P1 | |
ARHGEF15 | ENST00000421050.2 | c.2388G>T | p.Gly796= | synonymous_variant | 16/16 | 1 | P1 | ||
ARHGEF15 | ENST00000647883.1 | c.1851G>T | p.Gly617= | synonymous_variant | 13/13 |
Frequencies
GnomAD3 genomes ? AF: 0.00282 AC: 429AN: 152108Hom.: 5 Cov.: 32
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GnomAD3 exomes AF: 0.000697 AC: 175AN: 251092Hom.: 1 AF XY: 0.000560 AC XY: 76AN XY: 135730
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GnomAD4 exome AF: 0.000285 AC: 416AN: 1460458Hom.: 2 Cov.: 54 AF XY: 0.000253 AC XY: 184AN XY: 726526
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GnomAD4 genome ? AF: 0.00286 AC: 435AN: 152226Hom.: 5 Cov.: 32 AF XY: 0.00283 AC XY: 211AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at