Genetic Variant RBM23:c.*742C>T (chr14-22900988-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001352764.2(RBM23):c.*742C>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 0.15 in 151,964 control chromosomes in the GnomAD database, including 2,458 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 0.15 ( 2457 hom., cov: 31)

Exomes 𝑓: 0.095 ( 1 hom. )

Consequence

RBM23
NM_001352764.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.447

Publications

17 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:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352764.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RBM23	NM_001077351.2	MANE Select	c.*742C>T	3_prime_UTR	Exon 14 of 14	NP_001070819.1
RBM23	NM_001352764.2		c.*742C>T	3_prime_UTR	Exon 15 of 15	NP_001339693.1
RBM23	NM_001352763.2		c.*742C>T	3_prime_UTR	Exon 15 of 15	NP_001339692.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RBM23	ENST00000359890.8	TSL:1 MANE Select	c.*742C>T	3_prime_UTR	Exon 14 of 14	ENSP00000352956.3
RBM23	ENST00000399922.6	TSL:1	c.*742C>T	3_prime_UTR	Exon 13 of 13	ENSP00000382806.2
RBM23	ENST00000555209.5	TSL:1	c.*742C>T	3_prime_UTR	Exon 11 of 11	ENSP00000452602.1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22789

AN:

151804

Hom.:

2448

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.0482

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.0496

Gnomad EAS

AF:

0.0360

Gnomad SAS

AF:

0.0877

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0859

Gnomad OTH

AF:

0.120

GnomAD4 exome

AF:

0.0952

AC:

AN:

Hom.:

Cov.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.133

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.150

AC:

22828

AN:

151922

Hom.:

2457

Cov.:

AF XY:

0.152

AC XY:

11314

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.292

AC:

12083

AN:

41364

American (AMR)

AF:

0.139

AC:

2113

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.0496

AC:

172

AN:

3470

East Asian (EAS)

AF:

0.0357

AC:

185

AN:

5178

South Asian (SAS)

AF:

0.0869

AC:

419

AN:

4822

European-Finnish (FIN)

AF:

0.159

AC:

1682

AN:

10548

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0859

AC:

5841

AN:

67980

Other (OTH)

AF:

0.123

AC:

260

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

882

1763

2645

3526

4408

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.0969

Hom.:

426

Bravo

AF:

0.150

Asia WGS

AF:

0.103

AC:

361

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.71

(source)

DANN

Benign

0.45

PhyloP100

-0.45

Mutation Taster

=100/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over