Variant 14-63269159-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_020663.5(RHOJ):c.228C>T(p.Thr76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000961 in 1,611,352 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0011 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00095 ( 7 hom. )

Consequence

RHOJ
NM_020663.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.06

Variant links:

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]

RHOJ links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 14-63269159-C-T is Benign according to our data. Variant chr14-63269159-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2644275.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-6.06 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
RHOJ	NM_020663.5 linkuse as main transcript	c.228C>T	p.Thr76=	synonymous_variant	2/5	ENST00000316754.8
RHOJ	XM_047431613.1 linkuse as main transcript	c.228C>T	p.Thr76=	synonymous_variant	2/5
RHOJ	XM_011536993.4 linkuse as main transcript	c.228C>T	p.Thr76=	synonymous_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RHOJ	ENST00000316754.8 linkuse as main transcript	c.228C>T	p.Thr76=	synonymous_variant	2/5	1	NM_020663.5	P1	Q9H4E5-1
RHOJ	ENST00000555125.1 linkuse as main transcript	c.228C>T	p.Thr76=	synonymous_variant	2/4	2
RHOJ	ENST00000557133.1 linkuse as main transcript	n.413C>T		non_coding_transcript_exon_variant	2/2	2
RHOJ	ENST00000557447.5 linkuse as main transcript	c.228C>T	p.Thr76=	synonymous_variant, NMD_transcript_variant	2/5	5

Frequencies

GnomAD3 genomes

AF:

0.00110

AC:

168

AN:

152044

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00243

Gnomad ASJ

AF:

0.0214

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000515

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00152

AC:

382

AN:

250862

Hom.:

AF XY:

0.00141

AC XY:

191

AN XY:

135540

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.00130

Gnomad ASJ exome

AF:

0.0221

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000131

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000821

Gnomad OTH exome

AF:

0.00261

GnomAD4 exome

AF:

0.000947

AC:

1382

AN:

1459190

Hom.:

Cov.:

AF XY:

0.000945

AC XY:

686

AN XY:

726128

show subpopulations

Gnomad4 AFR exome

AF:

0.000389

Gnomad4 AMR exome

AF:

0.00165

Gnomad4 ASJ exome

AF:

0.0233

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000429

Gnomad4 OTH exome

AF:

0.00282

GnomAD4 genome

AF:

0.00110

AC:

167

AN:

152162

Hom.:

Cov.:

AF XY:

0.00122

AC XY:

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.000120

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.0214

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000515

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00273

Hom.:

Bravo

AF:

0.00154

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00125

EpiControl

AF:

0.00125

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

RHOJ: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.9

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over