rs10821851

Variant names:

• chr10-60901153-T-C
• rs10821851
• NM_014836.5:c.297-8158A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014836.5(RHOBTB1):​c.297-8158A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,082 control chromosomes in the GnomAD database, including 8,751 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 0.29 (8751 hom., cov: 33)
• Consequence: RHOBTB1 NM_014836.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 2 publications found

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]

LOC124902432 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014836.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHOBTB1	NM_014836.5	MANE Select	c.297-8158A>G		intron	N/A	NP_055651.1	O94844
	RHOBTB1	NM_001242359.2		c.297-8158A>G		intron	N/A	NP_001229288.1	O94844
	RHOBTB1	NM_001350902.2		c.297-8158A>G		intron	N/A	NP_001337831.1	O94844

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHOBTB1	ENST00000337910.10	TSL:1 MANE Select	c.297-8158A>G		intron	N/A	ENSP00000338671.5	O94844
	RHOBTB1	ENST00000924653.1		c.297-8158A>G		intron	N/A	ENSP00000594712.1
	RHOBTB1	ENST00000357917.4	TSL:2	c.297-8158A>G		intron	N/A	ENSP00000350595.4	O94844

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44166 AN: 151964 Hom.: 8732 Cov.: 33

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.291 AC: 44227 AN: 152082 Hom.: 8751 Cov.: 33 AF XY: 0.287 AC XY: 21352 AN XY: 74374

African (AFR) AF: 0.567 AC: 23509 AN: 41444

American (AMR) AF: 0.225 AC: 3448 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1319 AN: 5172

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4820

European-Finnish (FIN) AF: 0.139 AC: 1469 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11830 AN: 67974

Other (OTH) AF: 0.265 AC: 560 AN: 2116

Alfa AF: 0.319 Hom.: 4601

Bravo AF: 0.312

Asia WGS AF: 0.303 AC: 1052 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.48
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10821851; hg19: chr10-62660911;