rs1951119

chr14-22919117-A-Cchr14-22919117-A-Gchr14-22919117-A-T

Variant summary

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

The NM_001077351.2(RBM23):c.-129T>G variant causes a 5 prime UTR 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 NM_001077351.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

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]

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
RBM23	NM_001077351.2	c.-129T>G		5_prime_UTR_variant	1/14	ENST00000359890.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM23	ENST00000359890.8	c.-129T>G		5_prime_UTR_variant	1/14	1	NM_001077351.2	P2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86062 AN: 151844 Hom.: 25296 Cov.: 31

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: 60 AN: 88 Hom.: 24 Cov.: 0 AF XY: 0.667 AC XY: 48 AN XY: 72

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.671

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.567 AC: 86124 AN: 151964 Hom.: 25318 Cov.: 31 AF XY: 0.570 AC XY: 42361 AN XY: 74276

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.587

Alfa AF: 0.607 Hom.: 27064

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
Dann	Benign	0.45
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1951119; hg19: chr14-23388326;