chr13-49533153-T-C

Position:

• chr13-49533153-T-C

Variant summary

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

The ENST00000378302.7(RCBTB1):​c.*969A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,960 control chromosomes in the GnomAD database, including 17,638 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 0.48 (17638 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: RCBTB1 ENST00000378302.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

RCBTB1 (HGNC:18243): (RCC1 and BTB domain containing protein 1) This gene encodes a protein with an N-terminal RCC1 domain and a C-terminal BTB (broad complex, tramtrack and bric-a-brac) domain. In rat, over-expression of this gene in vascular smooth muscle cells induced cellular hypertrophy. In rat, the C-terminus of RCBTB1 interacts with the angiotensin II receptor-1A. In humans, this gene maps to a region of chromosome 13q that is frequently deleted in B-cell chronic lymphocytic leukemia and other lymphoid malignancies. [provided by RefSeq, Jul 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 (NFE) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RCBTB1	NM_018191.4	c.*969A>G		3_prime_UTR_variant	13/13	ENST00000378302.7	NP_060661.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RCBTB1	ENST00000378302.7	c.*969A>G		3_prime_UTR_variant	13/13	1	NM_018191.4	ENSP00000367552	P1
RCBTB1	ENST00000258646.3	c.*969A>G		3_prime_UTR_variant	11/11	2		ENSP00000258646	P1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72270 AN: 151842 Hom.: 17627 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.504

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.476 AC: 72317 AN: 151960 Hom.: 17638 Cov.: 31 AF XY: 0.473 AC XY: 35100 AN XY: 74266

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.501

Alfa AF: 0.521 Hom.: 25232

Bravo AF: 0.476

Asia WGS AF: 0.390 AC: 1353 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	5.3
DANN	Benign	0.67

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: rs1046028; hg19: chr13-50107289;