14-22905653-CCT-AGA

Variant names:

• chr14-22905653-CCT-AGA
• NM_001077351.2:c.406_408delAGGinsTCT
• RBM23 p.Arg136Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001077351.2(RBM23):​c.406_408delAGGinsTCT​(p.Arg136Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RBM23 NM_001077351.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077351.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM23	NM_001077351.2	MANE Select	c.406_408delAGGinsTCT	p.Arg136Ser	missense	N/A	NP_001070819.1	Q86U06-1
	RBM23	NM_001352764.2		c.538_540delAGGinsTCT	p.Arg180Ser	missense	N/A	NP_001339693.1
	RBM23	NM_001352763.2		c.406_408delAGGinsTCT	p.Arg136Ser	missense	N/A	NP_001339692.1	A0A0S2Z5D9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM23	ENST00000359890.8	TSL:1 MANE Select	c.406_408delAGGinsTCT	p.Arg136Ser	missense	N/A	ENSP00000352956.3	Q86U06-1
	RBM23	ENST00000399922.6	TSL:1	c.358_360delAGGinsTCT	p.Arg120Ser	missense	N/A	ENSP00000382806.2	Q86U06-2
	RBM23	ENST00000555209.5	TSL:1	c.-270-202_-270-200delAGGinsTCT		intron	N/A	ENSP00000452602.1	G3V5Z6

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr14-23374862;