Variant chr13-49540845-T-A 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.1455+31A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,605,926 control chromosomes in the GnomAD database, including 3,543 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.070 ( 463 hom., cov: 33)

Exomes 𝑓: 0.059 ( 3080 hom. )

Consequence

RCBTB1
NM_018191.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.10

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=-0.79).

BP6

Variant 13-49540845-T-A is Benign according to our data. Variant chr13-49540845-T-A is described in ClinVar as [Benign]. Clinvar id is 1277594.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RCBTB1	NM_018191.4 linkuse as main transcript	c.1455+31A>T		intron_variant		ENST00000378302.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RCBTB1	ENST00000378302.7 linkuse as main transcript	c.1455+31A>T		intron_variant		1	NM_018191.4	P1	Q8NDN9-1
RCBTB1	ENST00000258646.3 linkuse as main transcript	c.1455+31A>T		intron_variant		2		P1	Q8NDN9-1

Frequencies

GnomAD3 genomes

AF:

0.0696

AC:

10592

AN:

152134

Hom.:

463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.105

Gnomad AMI

AF:

0.0451

Gnomad AMR

AF:

0.0387

Gnomad ASJ

AF:

0.0343

Gnomad EAS

AF:

0.0539

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.0883

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.0517

Gnomad OTH

AF:

0.0474

GnomAD3 exomes

AF:

0.0686

AC:

16762

AN:

244460

Hom.:

721

AF XY:

0.0714

AC XY:

9434

AN XY:

132172

show subpopulations

Gnomad AFR exome

AF:

0.109

Gnomad AMR exome

AF:

0.0468

Gnomad ASJ exome

AF:

0.0323

Gnomad EAS exome

AF:

0.0622

Gnomad SAS exome

AF:

0.138

Gnomad FIN exome

AF:

0.0844

Gnomad NFE exome

AF:

0.0531

Gnomad OTH exome

AF:

0.0523

GnomAD4 exome

AF:

0.0590

AC:

85795

AN:

1453674

Hom.:

3080

Cov.:

AF XY:

0.0610

AC XY:

44057

AN XY:

722822

show subpopulations

Gnomad4 AFR exome

AF:

0.113

Gnomad4 AMR exome

AF:

0.0448

Gnomad4 ASJ exome

AF:

0.0314

Gnomad4 EAS exome

AF:

0.0435

Gnomad4 SAS exome

AF:

0.135

Gnomad4 FIN exome

AF:

0.0840

Gnomad4 NFE exome

AF:

0.0524

Gnomad4 OTH exome

AF:

0.0568

GnomAD4 genome

AF:

0.0696

AC:

10594

AN:

152252

Hom.:

463

Cov.:

AF XY:

0.0717

AC XY:

5337

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.105

Gnomad4 AMR

AF:

0.0386

Gnomad4 ASJ

AF:

0.0343

Gnomad4 EAS

AF:

0.0536

Gnomad4 SAS

AF:

0.136

Gnomad4 FIN

AF:

0.0883

Gnomad4 NFE

AF:

0.0517

Gnomad4 OTH

AF:

0.0459

Alfa

AF:

0.0579

Hom.:

Bravo

AF:

0.0663

Asia WGS

AF:

0.0960

AC:

333

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.14

DANN

Benign

0.73

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