rs2306080

chr3-28757966-A-Gchr3-28757966-A-T

Variant summary

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

The NR_038840.1(LINC00693):n.1283A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0632 in 152,260 control chromosomes in the GnomAD database, including 447 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 0.063 (447 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC00693 NR_038840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979

Genes affected

LINC00693 (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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00693	NR_038840.1	n.1283A>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBMS3	ENST00000636680.2	c.214-107258A>G		intron_variant		5
RBMS3	ENST00000432518.6	n.1770A>G		non_coding_transcript_exon_variant	5/5	5

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9604 AN: 152142 Hom.: 445 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.0707

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0632 AC: 9617 AN: 152260 Hom.: 447 Cov.: 32 AF XY: 0.0654 AC XY: 4870 AN XY: 74452

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.0572

Gnomad4 ASJ AF: 0.0913

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.0757

Alfa AF: 0.0627 Hom.: 189

Bravo AF: 0.0597

Asia WGS AF: 0.216 AC: 749 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.16
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: rs2306080; hg19: chr3-28799457;