chr3-29245271-A-G

Variant names:

• chr3-29245271-A-G
• rs9310888
• ENST00000635992.1:n.*582+62142A>G

Variant summary

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

The ENST00000635992.1(ENSG00000283563):​n.*582+62142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,034 control chromosomes in the GnomAD database, including 5,188 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 0.19 (5188 hom., cov: 32)
• Consequence: ENSG00000283563 ENST00000635992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 6 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]

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

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 (AFR) allele frequency at 95% confidence interval = 0.455 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.*582+62142A>G		intron_variant	Intron 8 of 13	5		ENSP00000489994.1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29182 AN: 151916 Hom.: 5178 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.192 AC: 29235 AN: 152034 Hom.: 5188 Cov.: 32 AF XY: 0.193 AC XY: 14372 AN XY: 74296

African (AFR) AF: 0.461 AC: 19085 AN: 41438

American (AMR) AF: 0.0987 AC: 1508 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1832 AN: 5166

South Asian (SAS) AF: 0.155 AC: 747 AN: 4810

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10590

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4150 AN: 67984

Other (OTH) AF: 0.160 AC: 336 AN: 2102

Alfa AF: 0.0946 Hom.: 878

Bravo AF: 0.204

Asia WGS AF: 0.277 AC: 964 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	1.6
DANN	Benign	0.41
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs9310888; hg19: chr3-29286762;