rs142667369
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_173728.4(ARHGEF15):c.1637G>A(p.Arg546Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000207 in 1,450,688 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
ARHGEF15
NM_173728.4 missense
NM_173728.4 missense
Scores
1
10
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.58
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARHGEF15 | NM_173728.4 | c.1637G>A | p.Arg546Gln | missense_variant | Exon 9 of 16 | ENST00000361926.8 | NP_776089.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARHGEF15 | ENST00000361926.8 | c.1637G>A | p.Arg546Gln | missense_variant | Exon 9 of 16 | 1 | NM_173728.4 | ENSP00000355026.3 | ||
ARHGEF15 | ENST00000421050.2 | c.1637G>A | p.Arg546Gln | missense_variant | Exon 9 of 16 | 1 | ENSP00000412505.1 | |||
ARHGEF15 | ENST00000647883.1 | c.1100G>A | p.Arg367Gln | missense_variant | Exon 6 of 13 | ENSP00000498197.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 234688Hom.: 0 AF XY: 0.00000776 AC XY: 1AN XY: 128918
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GnomAD4 exome AF: 0.00000207 AC: 3AN: 1450688Hom.: 0 Cov.: 33 AF XY: 0.00000139 AC XY: 1AN XY: 721996
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GnomAD4 genome Cov.: 31
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31
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.
REVEL
Uncertain
Sift
Benign
D;D;.
Sift4G
Uncertain
D;D;.
Polyphen
D;D;.
Vest4
MutPred
Gain of ubiquitination at K543 (P = 0.0544);Gain of ubiquitination at K543 (P = 0.0544);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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