rs17024608

Variant names:

• chr3-29913199-A-G
• rs17024608
• NM_001003793.3:c.939+13444A>G

Variant summary

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

The NM_001003793.3(RBMS3):​c.939+13444A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0784 in 152,084 control chromosomes in the GnomAD database, including 529 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 0.078 (529 hom., cov: 32)
• Consequence: RBMS3 NM_001003793.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 8 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 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.939+13444A>G		intron	N/A	NP_001003793.1
	RBMS3	NM_001330696.1		c.936+13444A>G		intron	N/A	NP_001317625.1
	RBMS3	NM_001177712.2		c.978+13444A>G		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.939+13444A>G		intron	N/A	ENSP00000373277.2
	RBMS3	ENST00000456853.1	TSL:1	c.978+13444A>G		intron	N/A	ENSP00000400519.1
	RBMS3	ENST00000273139.13	TSL:1	c.939+13444A>G		intron	N/A	ENSP00000273139.9

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11907 AN: 151966 Hom.: 527 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0784 AC: 11920 AN: 152084 Hom.: 529 Cov.: 32 AF XY: 0.0785 AC XY: 5836 AN XY: 74360

African (AFR) AF: 0.0708 AC: 2939 AN: 41492

American (AMR) AF: 0.0687 AC: 1046 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5166

South Asian (SAS) AF: 0.109 AC: 524 AN: 4828

European-Finnish (FIN) AF: 0.0874 AC: 929 AN: 10626

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0876 AC: 5954 AN: 67954

Other (OTH) AF: 0.0896 AC: 189 AN: 2110

Alfa AF: 0.0842 Hom.: 2076

Bravo AF: 0.0758

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.69
PhyloP100		0.0
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: rs17024608; hg19: chr3-29954690;