10-60901153-T-C

Position:

• chr10-60901153-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RHOBTB1	NM_014836.5	c.297-8158A>G		intron_variant		ENST00000337910.10
LOC124902432	XR_007062152.1	n.155+113T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RHOBTB1	ENST00000337910.10	c.297-8158A>G		intron_variant		1	NM_014836.5	P1
RHOBTB1	ENST00000357917.4	c.297-8158A>G		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.265

Alfa AF: 0.228 Hom.: 1112

Bravo AF: 0.312

Asia WGS AF: 0.303 AC: 1052 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.48

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: rs10821851; hg19: chr10-62660911;