rs17177789

Positions:

• chr14-63212991-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• 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]

ACMG classification

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: 27949 AN: 152002 Hom.: 3057 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.208

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.184 AC: 27955 AN: 152120 Hom.: 3056 Cov.: 32 AF XY: 0.180 AC XY: 13375 AN XY: 74358

Gnomad4 AFR AF: 0.0618

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.208

Alfa AF: 0.241 Hom.: 6374

Bravo AF: 0.181

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.2
DANN	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17177789; hg19: chr14-63679709;