dbSNP rs1951119: RBM23:n.20T>G (chr14-22919117-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000557667.5(RBM23):n.20T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 152,052 control chromosomes in the GnomAD database, including 25,342 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 0.57 ( 25318 hom., cov: 31)

Exomes 𝑓: 0.68 ( 24 hom. )

Consequence

RBM23
ENST00000557667.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.344

Publications

20 publications found

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:

PRMT5-AS1 (HGNC:40533): (PRMT5 antisense RNA 1)

PRMT5-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM23	NM_001077351.2 link	c.-129T>G		5_prime_UTR_variant	Exon 1 of 14	ENST00000359890.8	NP_001070819.1	Q86U06-1A0A0S2Z5D9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM23	ENST00000359890.8 link	c.-129T>G		5_prime_UTR_variant	Exon 1 of 14	1	NM_001077351.2	ENSP00000352956.3		Q86U06-1

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

86062

AN:

151844

Hom.:

25296

Cov.:

show subpopulations

Gnomad AFR

AF:

0.418

Gnomad AMI

AF:

0.727

Gnomad AMR

AF:

0.597

Gnomad ASJ

AF:

0.573

Gnomad EAS

AF:

0.791

Gnomad SAS

AF:

0.752

Gnomad FIN

AF:

0.591

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.590

GnomAD4 exome

AF:

0.682

AC:

AN:

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.671

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.567

AC:

86124

AN:

151964

Hom.:

25318

Cov.:

AF XY:

0.570

AC XY:

42361

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.418

AC:

17321

AN:

41452

American (AMR)

AF:

0.597

AC:

9119

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.573

AC:

1987

AN:

3470

East Asian (EAS)

AF:

0.792

AC:

4083

AN:

5158

South Asian (SAS)

AF:

0.754

AC:

3635

AN:

4822

European-Finnish (FIN)

AF:

0.591

AC:

6230

AN:

10534

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.613

AC:

41661

AN:

67954

Other (OTH)

AF:

0.587

AC:

1233

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1844

3688

5532

7376

9220

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

746

1492

2238

2984

3730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.600

Hom.:

35061

Bravo

AF:

0.561

Asia WGS

AF:

0.736

AC:

2559

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.3

(source)

DANN

Benign

0.45

PhyloP100

0.34

PromoterAI

-0.023

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over