3-28979918-C-T

Position:

• chr3-28979918-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635992.1(ENSG00000283563):​n.*408+114626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,194 control chromosomes in the GnomAD database, including 63,312 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 0.91 (63312 hom., cov: 32)
• Consequence: ENSG00000283563 ENST00000635992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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

Verdict is Benign. Variant got -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 = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.28979918C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283563	ENST00000635992.1	n.*408+114626C>T		intron_variant		5		ENSP00000489994.1

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138551 AN: 152076 Hom.: 63262 Cov.: 32

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.911 AC: 138659 AN: 152194 Hom.: 63312 Cov.: 32 AF XY: 0.913 AC XY: 67953 AN XY: 74408

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.925

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.897

Alfa AF: 0.900 Hom.: 10686

Bravo AF: 0.913

Asia WGS AF: 0.948 AC: 3292 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6549904; hg19: chr3-29021409;