rs1392702
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_019555.3(ARHGEF3):c.96+1752A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
ARHGEF3
NM_019555.3 intron
NM_019555.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.550
Publications
0 publications found
Genes affected
ARHGEF3 (HGNC:683): (Rho guanine nucleotide exchange factor 3) Rho-like GTPases are involved in a variety of cellular processes, and they are activated by binding GTP and inactivated by conversion of GTP to GDP by their intrinsic GTPase activity. Guanine nucleotide exchange factors (GEFs) accelerate the GTPase activity of Rho GTPases by catalyzing their release of bound GDP. This gene encodes a guanine nucleotide exchange factor, which specifically activates two members of the Rho GTPase family: RHOA and RHOB, both of which have a role in bone cell biology. It has been identified that genetic variation in this gene plays a role in the determination of bone mineral density (BMD), indicating the implication of this gene in postmenopausal osteoporosis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_019555.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ARHGEF3 | TSL:1 MANE Select | c.96+1752A>T | intron | N/A | ENSP00000296315.3 | Q9NR81-1 | |||
| ARHGEF3 | TSL:1 | c.193-26135A>T | intron | N/A | ENSP00000341071.4 | Q9NR81-2 | |||
| ARHGEF3 | TSL:1 | c.96+1752A>T | intron | N/A | ENSP00000417986.1 | C9J586 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 152020Hom.: 0 Cov.: 32
GnomAD3 genomes
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152020
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00 AC: 0AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74254
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
152020
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74254
African (AFR)
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0
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41412
American (AMR)
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0
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15270
Ashkenazi Jewish (ASJ)
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0
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3470
East Asian (EAS)
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0
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5194
South Asian (SAS)
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0
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4822
European-Finnish (FIN)
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0
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10564
Middle Eastern (MID)
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0
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316
European-Non Finnish (NFE)
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0
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67970
Other (OTH)
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0
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2090
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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