NM_006743.5:c.-13-57C>A

Variant names:

• chrX-48575111-C-A
• rs2249583
• NM_006743.5:c.-13-57C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006743.5(RBM3):​c.-13-57C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: RBM3 NM_006743.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 8 publications found

Genes affected

RBM3 (HGNC:9900): (RNA binding motif protein 3) This gene is a member of the glycine-rich RNA-binding protein family and encodes a protein with one RNA recognition motif (RRM) domain. Expression of this gene is induced by cold shock and low oxygen tension. A pseudogene exists on chromosome 1. Multiple alternatively spliced transcript variants that are predicted to encode different isoforms have been characterized although some of these variants fit nonsense-mediated decay (NMD) criteria. [provided by RefSeq, Jul 2008]

ENSG00000204620 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM3	NM_006743.5	c.-13-57C>A		intron_variant	Intron 1 of 6	ENST00000376759.8	NP_006734.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM3	ENST00000376759.8	c.-13-57C>A		intron_variant	Intron 1 of 6	1	NM_006743.5	ENSP00000365950.3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 769138 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 214314

African (AFR) AF: 0.00 AC: 0 AN: 19339

American (AMR) AF: 0.00 AC: 0 AN: 27793

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16830

East Asian (EAS) AF: 0.00 AC: 0 AN: 26603

South Asian (SAS) AF: 0.00 AC: 0 AN: 43969

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36997

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3508

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 558896

Other (OTH) AF: 0.00 AC: 0 AN: 35203

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.52
DANN	Benign	0.60
PhyloP100		-1.9
PromoterAI		-0.0081	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.95

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

Other links and lift over

dbSNP: rs2249583; hg19: chrX-48433499;