rs1013704

Variant names:

• chr10-60937660-G-C
• rs1013704
• NM_014836.5:c.-11+4144C>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.-11+4144C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 152,218 control chromosomes in the GnomAD database, including 279 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 0.047 (279 hom., cov: 32)
• Consequence: RHOBTB1 NM_014836.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0995 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RHOBTB1	NM_014836.5	c.-11+4144C>G		intron_variant	Intron 2 of 10	ENST00000337910.10	NP_055651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RHOBTB1	ENST00000337910.10	c.-11+4144C>G		intron_variant	Intron 2 of 10	1	NM_014836.5	ENSP00000338671.5
RHOBTB1	ENST00000357917.4	c.-11+4144C>G		intron_variant	Intron 3 of 11	2		ENSP00000350595.4

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7065 AN: 152100 Hom.: 277 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0383

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0197

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0465 AC: 7081 AN: 152218 Hom.: 279 Cov.: 32 AF XY: 0.0463 AC XY: 3444 AN XY: 74424

African (AFR) AF: 0.102 AC: 4237 AN: 41520

American (AMR) AF: 0.0360 AC: 551 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 38 AN: 3472

East Asian (EAS) AF: 0.0386 AC: 200 AN: 5180

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4828

European-Finnish (FIN) AF: 0.0197 AC: 209 AN: 10600

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0234 AC: 1591 AN: 68006

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0367 Hom.: 14

Bravo AF: 0.0504

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.4
DANN	Benign	0.69
PhyloP100		0.45
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: rs1013704; hg19: chr10-62697418;