Variant rs1570342 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001077351.2(RBM23):c.*2754G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,876 control chromosomes in the GnomAD database, including 8,669 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 0.32 ( 8666 hom., cov: 31)

Exomes 𝑓: 0.33 ( 3 hom. )

Consequence

RBM23
NM_001077351.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.259

Variant links:

Genes affected

RBM23 (HGNC:20155): (RNA binding motif protein 23) This gene encodes a member of the U2AF-like family of RNA binding proteins. This protein interacts with some steroid nuclear receptors, localizes to the promoter of a steroid- responsive gene, and increases transcription of steroid-responsive transcriptional reporters in a hormone-dependent manner. It is also implicated in the steroid receptor-dependent regulation of alternative splicing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

RBM23 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM23	NM_001077351.2 linkuse as main transcript	c.*2754G>T		3_prime_UTR_variant	14/14	ENST00000359890.8	NP_001070819.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM23	ENST00000359890.8 linkuse as main transcript	c.*2754G>T		3_prime_UTR_variant	14/14	1	NM_001077351.2	ENSP00000352956	P2	Q86U06-1

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48367

AN:

151706

Hom.:

8654

Cov.:

show subpopulations

Gnomad AFR

AF:

0.484

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.282

GnomAD4 exome

AF:

0.327

AC:

AN:

Hom.:

Cov.:

AF XY:

0.306

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.310

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.319

AC:

48412

AN:

151824

Hom.:

8666

Cov.:

AF XY:

0.319

AC XY:

23689

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.484

Gnomad4 AMR

AF:

0.280

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.220

Gnomad4 SAS

AF:

0.215

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.255

Gnomad4 OTH

AF:

0.285

Alfa

AF:

0.236

Hom.:

2366

Bravo

AF:

0.322

Asia WGS

AF:

0.236

AC:

820

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.4

DANN

Benign

0.60

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over