rs10510615

Variant names:

• chr3-28833769-T-C
• rs10510615
• ENST00000635992.1:n.*340-31455T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-28833769-T-C
• chr3-28833769-T-G

Variant summary

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

The ENST00000635992.1(ENSG00000283563):​n.*340-31455T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0257 in 152,304 control chromosomes in the GnomAD database, including 100 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 0.026 (100 hom., cov: 32)
• Consequence: ENSG00000283563 ENST00000635992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459
• Publications: 0 publications found

Genes affected

ENSG00000283563 (HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283563	ENST00000635992.1	n.*340-31455T>C		intron_variant	Intron 6 of 13	5		ENSP00000489994.1
RBMS3	ENST00000636680.2	c.214-31455T>C		intron_variant	Intron 1 of 16	5		ENSP00000490271.2

Frequencies

GnomAD3 genomes AF: 0.0256 AC: 3898 AN: 152186 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.00433

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0118

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0257 AC: 3909 AN: 152304 Hom.: 100 Cov.: 32 AF XY: 0.0268 AC XY: 1997 AN XY: 74464

African (AFR) AF: 0.0307 AC: 1277 AN: 41566

American (AMR) AF: 0.0635 AC: 971 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3470

East Asian (EAS) AF: 0.0617 AC: 319 AN: 5174

South Asian (SAS) AF: 0.0505 AC: 244 AN: 4832

European-Finnish (FIN) AF: 0.00433 AC: 46 AN: 10620

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.0118 AC: 805 AN: 68032

Other (OTH) AF: 0.0388 AC: 82 AN: 2114

Alfa AF: 0.0150 Hom.: 14

Bravo AF: 0.0297

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.48
PhyloP100		-0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10510615; hg19: chr3-28875260;