rs16659

Positions:

• chr13-49533070-AAAAGTGAAAGATGAT-A
• chr13-49533070-AAAAGTGAAAGATGAT-AAAAGTGAAAGATGATAAAGTGAAAGATGAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_018191.4(RCBTB1):​c.*1037_*1051del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.47 (17528 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: RCBTB1 NM_018191.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.62

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RCBTB1	NM_018191.4	c.*1037_*1051del		3_prime_UTR_variant	13/13	ENST00000378302.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RCBTB1	ENST00000378302.7	c.*1037_*1051del		3_prime_UTR_variant	13/13	1	NM_018191.4	P1
RCBTB1	ENST00000258646.3	c.*1037_*1051del		3_prime_UTR_variant	11/11	2		P1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72012 AN: 151596 Hom.: 17516 Cov.: 0

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.475 AC: 72061 AN: 151716 Hom.: 17528 Cov.: 0 AF XY: 0.471 AC XY: 34953 AN XY: 74138

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.500

Alfa AF: 0.497 Hom.: 2035

Bravo AF: 0.476

Asia WGS AF: 0.390 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16659; hg19: chr13-50107206;