3-28678635-C-T

Variant names:

• chr3-28678635-C-T
• rs17651822
• ENST00000635992.1:n.*339+102139C>T

Variant summary

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

The ENST00000635992.1(ENSG00000283563):​n.*339+102139C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,172 control chromosomes in the GnomAD database, including 1,050 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 0.10 (1050 hom., cov: 32)
• Consequence: ENSG00000283563 ENST00000635992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 4 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]

LINC00693 (HGNC:44526): (long intergenic non-protein coding RNA 693)

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 = 0.174 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635992.1. 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
	LINC00693	NR_038840.1		n.323-78123C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283563	ENST00000635992.1	TSL:5	n.*339+102139C>T		intron	N/A	ENSP00000489994.1	A0A1B0GU75
	RBMS3	ENST00000636680.2	TSL:5	c.213+102139C>T		intron	N/A	ENSP00000490271.2	A0A1B0GUW5
	RBMS3	ENST00000432518.6	TSL:5	n.810-78123C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15506 AN: 152054 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.102 AC: 15496 AN: 152172 Hom.: 1050 Cov.: 32 AF XY: 0.102 AC XY: 7599 AN XY: 74392

African (AFR) AF: 0.0237 AC: 986 AN: 41538

American (AMR) AF: 0.0833 AC: 1273 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.0886 AC: 457 AN: 5158

South Asian (SAS) AF: 0.184 AC: 889 AN: 4822

European-Finnish (FIN) AF: 0.137 AC: 1450 AN: 10586

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9382 AN: 68004

Other (OTH) AF: 0.114 AC: 240 AN: 2104

Alfa AF: 0.123 Hom.: 4173

Bravo AF: 0.0936

Asia WGS AF: 0.107 AC: 372 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	0.79
PhyloP100		0.0020

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17651822;

hg19: chr3-28720126;