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

Variant names:

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

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>T 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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006743.5. 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
	RBM3	NM_006743.5	MANE Select	c.-13-57C>T		intron	N/A	NP_006734.1	P98179

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM3	ENST00000376759.8	TSL:1 MANE Select	c.-13-57C>T		intron	N/A	ENSP00000365950.3	P98179
	RBM3	ENST00000491240.5	TSL:1	n.51-57C>T		intron	N/A
	RBM3	ENST00000376755.1	TSL:2	c.-70C>T		5_prime_UTR	Exon 1 of 6	ENSP00000365946.1	P98179

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: 214312

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: 36996

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

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 558897

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

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 3654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.64
DANN	Benign	0.67
PhyloP100		-1.9
PromoterAI		0.021	Neutral

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;