1-110343114-G-A

Variant names:

• chr1-110343114-G-A
• rs1572263
• NM_022768.5:c.2863+846G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_022768.5(RBM15):​c.2863+846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,044 control chromosomes in the GnomAD database, including 46,294 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 0.78 (46294 hom., cov: 32)
• Consequence: RBM15 NM_022768.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 11 publications found

Genes affected

RBM15 (HGNC:14959): (RNA binding motif protein 15) Members of the SPEN (Split-end) family of proteins, including RBM15, have repressor function in several signaling pathways and may bind to RNA through interaction with spliceosome components (Hiriart et al., 2005 [PubMed 16129689]).[supplied by OMIM, Feb 2009]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022768.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM15	NM_022768.5	MANE Select	c.2863+846G>A		intron	N/A	NP_073605.4
	RBM15	NM_001201545.2		c.2863+846G>A		intron	N/A	NP_001188474.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM15	ENST00000369784.9	TSL:1 MANE Select	c.2863+846G>A		intron	N/A	ENSP00000358799.3
	RBM15	ENST00000618772.4	TSL:1	c.2863+846G>A		intron	N/A	ENSP00000483133.1
	RBM15	ENST00000487146.8	TSL:1	c.2863+846G>A		intron	N/A	ENSP00000473552.3

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117969 AN: 151926 Hom.: 46242 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.777 AC: 118080 AN: 152044 Hom.: 46294 Cov.: 32 AF XY: 0.775 AC XY: 57598 AN XY: 74322

African (AFR) AF: 0.887 AC: 36824 AN: 41510

American (AMR) AF: 0.800 AC: 12208 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2378 AN: 3468

East Asian (EAS) AF: 0.760 AC: 3933 AN: 5174

South Asian (SAS) AF: 0.796 AC: 3843 AN: 4828

European-Finnish (FIN) AF: 0.676 AC: 7130 AN: 10540

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49383 AN: 67940

Other (OTH) AF: 0.743 AC: 1570 AN: 2112

Alfa AF: 0.741 Hom.: 186511

Bravo AF: 0.788

Asia WGS AF: 0.757 AC: 2634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1572263; hg19: chr1-110885736;