NM_001003793.3:c.308-34519C>A

Variant names:

• chr3-29552595-C-A
• rs28150
• NM_001003793.3:c.308-34519C>A

Variant summary

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

The NM_001003793.3(RBMS3):​c.308-34519C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,852 control chromosomes in the GnomAD database, including 22,953 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 0.54 (22953 hom., cov: 31)
• Consequence: RBMS3 NM_001003793.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBMS3	NM_001003793.3	MANE Select	c.308-34519C>A		intron	N/A	NP_001003793.1	Q6XE24-1
	RBMS3	NM_001330696.1		c.305-34519C>A		intron	N/A	NP_001317625.1	C9JIJ9
	RBMS3	NM_001177712.2		c.308-34519C>A		intron	N/A	NP_001171183.1	Q6XE24-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBMS3	ENST00000383767.7	TSL:1 MANE Select	c.308-34519C>A		intron	N/A	ENSP00000373277.2	Q6XE24-1
	RBMS3	ENST00000456853.1	TSL:1	c.308-34519C>A		intron	N/A	ENSP00000400519.1	Q6XE24-2
	RBMS3	ENST00000273139.13	TSL:1	c.308-34519C>A		intron	N/A	ENSP00000273139.9	Q6XE24-4

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82159 AN: 151730 Hom.: 22940 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.541 AC: 82221 AN: 151852 Hom.: 22953 Cov.: 31 AF XY: 0.533 AC XY: 39552 AN XY: 74206

African (AFR) AF: 0.653 AC: 27071 AN: 41430

American (AMR) AF: 0.446 AC: 6799 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1329 AN: 5154

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4808

European-Finnish (FIN) AF: 0.483 AC: 5085 AN: 10518

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.537 AC: 36448 AN: 67894

Other (OTH) AF: 0.540 AC: 1142 AN: 2116

Alfa AF: 0.540 Hom.: 2841

Bravo AF: 0.544

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.68
PhyloP100		-0.047
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: rs28150; hg19: chr3-29594086;