rs17177789
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020663.5(RHOJ):c.178+7944C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,120 control chromosomes in the GnomAD database, including 3,056 homozygotes. 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 0.18 ( 3056 hom., cov: 32)
Consequence
RHOJ
NM_020663.5 intron
NM_020663.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.293
Genes affected
RHOJ (HGNC:688): (ras homolog family member J) This gene encodes one of the many small GTP-binding proteins in the Rho family shown to be associated with focal adhesions in endothelial cells (PMID: 21148427, 22103495). The encoded protein is activated by vascular endothelial growth factor and may regulate angiogenesis. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHOJ | NM_020663.5 | c.178+7944C>A | intron_variant | ENST00000316754.8 | |||
RHOJ | XM_011536993.4 | c.178+7944C>A | intron_variant | ||||
RHOJ | XM_047431613.1 | c.178+7944C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHOJ | ENST00000316754.8 | c.178+7944C>A | intron_variant | 1 | NM_020663.5 | P1 | |||
RHOJ | ENST00000555125.1 | c.178+7944C>A | intron_variant | 2 | |||||
RHOJ | ENST00000557447.5 | c.178+7944C>A | intron_variant, NMD_transcript_variant | 5 | |||||
RHOJ | ENST00000557133.1 | n.363+7944C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.184 AC: 27949AN: 152002Hom.: 3057 Cov.: 32
GnomAD3 genomes
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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 ? AF: 0.184 AC: 27955AN: 152120Hom.: 3056 Cov.: 32 AF XY: 0.180 AC XY: 13375AN XY: 74358
GnomAD4 genome
?
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27955
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152120
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32
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13375
AN XY:
74358
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486
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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