NM_001003793.3:c.307+45473G>T

Variant names:

• chr3-29533972-G-T
• rs1530057
• NM_001003793.3:c.307+45473G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001003793.3(RBMS3):​c.307+45473G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0459 in 152,202 control chromosomes in the GnomAD database, including 208 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 0.046 (208 hom., cov: 32)
• Consequence: RBMS3 NM_001003793.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 17 publications found

Genes affected

RBMS3 (HGNC:13427): (RNA binding motif single stranded interacting protein 3) This gene encodes an RNA-binding protein that belongs to the c-myc gene single-strand binding protein family. These proteins are characterized by the presence of two sets of ribonucleoprotein consensus sequence (RNP-CS) that contain conserved motifs, RNP1 and RNP2, originally described in RNA binding proteins, and required for DNA binding. These proteins have been implicated in such diverse functions as DNA replication, gene transcription, cell cycle progression and apoptosis. The encoded protein was isolated by virtue of its binding to an upstream element of the alpha2(I) collagen promoter. The observation that this protein localizes mostly in the cytoplasm suggests that it may be involved in a cytoplasmic function such as controlling RNA metabolism, rather than transcription. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]

ENSG00000283563 (HGNC:):

RBMS3-AS2 (HGNC:39988): (RBMS3 antisense RNA 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0951 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001003793.3. 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
	RBMS3	NM_001003793.3	MANE Select	c.307+45473G>T		intron	N/A	NP_001003793.1
	RBMS3	NM_001330696.1		c.304+45473G>T		intron	N/A	NP_001317625.1
	RBMS3	NM_001177712.2		c.307+45473G>T		intron	N/A	NP_001171183.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBMS3	ENST00000383767.7	TSL:1 MANE Select	c.307+45473G>T		intron	N/A	ENSP00000373277.2
	RBMS3	ENST00000456853.1	TSL:1	c.307+45473G>T		intron	N/A	ENSP00000400519.1
	RBMS3	ENST00000273139.13	TSL:1	c.307+45473G>T		intron	N/A	ENSP00000273139.9

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6988 AN: 152084 Hom.: 207 Cov.: 32

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0540

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0558

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0459 AC: 6990 AN: 152202 Hom.: 208 Cov.: 32 AF XY: 0.0456 AC XY: 3391 AN XY: 74406

African (AFR) AF: 0.0152 AC: 631 AN: 41526

American (AMR) AF: 0.0512 AC: 782 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0540 AC: 187 AN: 3466

East Asian (EAS) AF: 0.0776 AC: 402 AN: 5182

South Asian (SAS) AF: 0.103 AC: 495 AN: 4828

European-Finnish (FIN) AF: 0.0427 AC: 451 AN: 10570

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0558 AC: 3796 AN: 68032

Other (OTH) AF: 0.0568 AC: 120 AN: 2112

Alfa AF: 0.0539 Hom.: 1134

Bravo AF: 0.0441

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		0.037
Mutation Taster		=100/0	polymorphism (auto)

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: rs1530057; hg19: chr3-29575463;