rs7083122

chr10-60875947-C-A

Variant summary

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

The NM_014836.5(RHOBTB1):c.1727-905G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,098 control chromosomes in the GnomAD database, including 6,851 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 0.27 (6851 hom., cov: 33)
• Consequence: RHOBTB1 NM_014836.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

Genes affected

RHOBTB1 (HGNC:18738): (Rho related BTB domain containing 1) The protein encoded by this gene belongs to the Rho family of the small GTPase superfamily. It contains a GTPase domain, a proline-rich region, a tandem of 2 BTB (broad complex, tramtrack, and bric-a-brac) domains, and a conserved C-terminal region. The protein plays a role in small GTPase-mediated signal transduction and the organization of the actin filament system. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHOBTB1	NM_014836.5	c.1727-905G>T		intron_variant		ENST00000337910.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RHOBTB1	ENST00000337910.10	c.1727-905G>T		intron_variant		1	NM_014836.5	P1
RHOBTB1	ENST00000357917.4	c.1727-905G>T		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41244 AN: 151980 Hom.: 6828 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.272 AC: 41308 AN: 152098 Hom.: 6851 Cov.: 33 AF XY: 0.268 AC XY: 19950 AN XY: 74352

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.259

Alfa AF: 0.264 Hom.: 1254

Bravo AF: 0.285

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.47
Dann	Benign	0.74

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: rs7083122; hg19: chr10-62635705;