Variant 13-49534116-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018191.4(RCBTB1):c.*6A>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 0.514 in 1,611,914 control chromosomes in the GnomAD database, including 216,382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 18121 hom., cov: 31)

Exomes 𝑓: 0.52 ( 198261 hom. )

Consequence

RCBTB1
NM_018191.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.46

Variant links:

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]

RCBTB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 13-49534116-T-C is Benign according to our data. Variant chr13-49534116-T-C is described in ClinVar as [Benign]. Clinvar id is 1265543.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RCBTB1	NM_018191.4 link	c.*6A>G		3_prime_UTR_variant	13/13	ENST00000378302.7	NP_060661.3	Q8NDN9-1B3KR20

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
RCBTB1	ENST00000378302 link	c.*6A>G	3_prime_UTR_variant	13/13	1	NM_018191.4	ENSP00000367552.2	Q8NDN9-1
RCBTB1	ENST00000258646 link	c.*6A>G	3_prime_UTR_variant	11/11	2		ENSP00000258646.3	Q8NDN9-1
RCBTB1	ENST00000471984.1 link	n.490A>G	non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes

AF:

0.484

AC:

73463

AN:

151816

Hom.:

18107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.527

Gnomad ASJ

AF:

0.545

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.529

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.512

GnomAD3 exomes

AF:

0.495

AC:

123937

AN:

250412

Hom.:

31523

AF XY:

0.488

AC XY:

66070

AN XY:

135370

show subpopulations

Gnomad AFR exome

AF:

0.384

Gnomad AMR exome

AF:

0.532

Gnomad ASJ exome

AF:

0.566

Gnomad EAS exome

AF:

0.479

Gnomad SAS exome

AF:

0.316

Gnomad FIN exome

AF:

0.539

Gnomad NFE exome

AF:

0.534

Gnomad OTH exome

AF:

0.527

GnomAD4 exome

AF:

0.517

AC:

755158

AN:

1459980

Hom.:

198261

Cov.:

AF XY:

0.513

AC XY:

372360

AN XY:

726286

show subpopulations

Gnomad4 AFR exome

AF:

0.386

Gnomad4 AMR exome

AF:

0.529

Gnomad4 ASJ exome

AF:

0.569

Gnomad4 EAS exome

AF:

0.495

Gnomad4 SAS exome

AF:

0.318

Gnomad4 FIN exome

AF:

0.535

Gnomad4 NFE exome

AF:

0.535

Gnomad4 OTH exome

AF:

0.514

GnomAD4 genome

AF:

0.484

AC:

73513

AN:

151934

Hom.:

18121

Cov.:

AF XY:

0.480

AC XY:

35652

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.390

Gnomad4 AMR

AF:

0.527

Gnomad4 ASJ

AF:

0.545

Gnomad4 EAS

AF:

0.473

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.529

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.510

Alfa

AF:

0.525

Hom.:

26757

Bravo

AF:

0.485

Asia WGS

AF:

0.393

AC:

1364

AN:

3478

EpiCase

AF:

0.539

EpiControl

AF:

0.534

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

RCBTB1-related retinopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.22

DANN

Benign

0.53

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over