rs7469

Positions:

• chr14-22900988-G-A
• chr14-22900988-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001077351.2(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_001077351.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM23	NM_001077351.2	c.*742C>T		3_prime_UTR_variant	14/14	ENST00000359890.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM23	ENST00000359890.8	c.*742C>T		3_prime_UTR_variant	14/14	1	NM_001077351.2	P2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22789 AN: 151804 Hom.: 2448 Cov.: 31

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: 4 AN: 42 Hom.: 1 Cov.: 0 AF XY: 0.100 AC XY: 3 AN XY: 30

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.150 AC: 22828 AN: 151922 Hom.: 2457 Cov.: 31 AF XY: 0.152 AC XY: 11314 AN XY: 74260

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0496

Gnomad4 EAS AF: 0.0357

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.0859

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0871 Hom.: 229

Bravo AF: 0.150

Asia WGS AF: 0.103 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.71
DANN	Benign	0.45

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

Other links and lift over

dbSNP: rs7469; hg19: chr14-23370197;