chr3-29315572-C-T

Variant names:

• chr3-29315572-C-T
• rs6549924
• NM_001003793.3:c.75+33816C>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.75+33816C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,466 control chromosomes in the GnomAD database, including 13,306 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 0.41 (13306 hom., cov: 32)
• Consequence: RBMS3 NM_001003793.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 0 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:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 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.75+33816C>T		intron	N/A	NP_001003793.1
	RBMS3	NM_001330696.1		c.75+33816C>T		intron	N/A	NP_001317625.1
	RBMS3	NM_001177712.2		c.75+33816C>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.75+33816C>T		intron	N/A	ENSP00000373277.2
	RBMS3	ENST00000456853.1	TSL:1	c.75+33816C>T		intron	N/A	ENSP00000400519.1
	RBMS3	ENST00000273139.13	TSL:1	c.75+33816C>T		intron	N/A	ENSP00000273139.9

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61393 AN: 151346 Hom.: 13302 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.406 AC: 61431 AN: 151466 Hom.: 13306 Cov.: 32 AF XY: 0.416 AC XY: 30788 AN XY: 74006

African (AFR) AF: 0.361 AC: 14926 AN: 41398

American (AMR) AF: 0.560 AC: 8491 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1145 AN: 3446

East Asian (EAS) AF: 0.764 AC: 3915 AN: 5124

South Asian (SAS) AF: 0.607 AC: 2927 AN: 4822

European-Finnish (FIN) AF: 0.388 AC: 4080 AN: 10528

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24626 AN: 67686

Other (OTH) AF: 0.415 AC: 870 AN: 2098

Alfa AF: 0.381 Hom.: 32980

Bravo AF: 0.410

Asia WGS AF: 0.662 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		-0.026
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: rs6549924; hg19: chr3-29357063;