3-29187381-A-G

Variant summary

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

The ENST00000655701.1(RBMS3-AS3):n.354+86942T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.943 in 151,884 control chromosomes in the GnomAD database, including 67,659 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 0.94 (67659 hom., cov: 30)
• Consequence: RBMS3-AS3 ENST00000655701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

Genes affected

RBMS3-AS3 (HGNC:39989): (RBMS3 antisense RNA 3)

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBMS3-AS3	ENST00000655701.1	n.354+86942T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.943 AC: 143046 AN: 151766 Hom.: 67598 Cov.: 30

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.943 AC: 143165 AN: 151884 Hom.: 67659 Cov.: 30 AF XY: 0.939 AC XY: 69719 AN XY: 74226

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.975

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.957

Alfa AF: 0.940 Hom.: 12165

Bravo AF: 0.951

Asia WGS AF: 0.825 AC: 2870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	0.98
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1517144; hg19: chr3-29228872;