rs732982

chr18-57060228-G-A

Variant summary

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

The NR_152602.1(LINC-ROR):n.411-3542C>T 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 0.258 in 152,088 control chromosomes in the GnomAD database, including 6,364 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 0.26 (6364 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC-ROR NR_152602.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.16

Genes affected

LINC-ROR (HGNC:43773): (long intergenic non-protein coding RNA, regulator of reprogramming) This gene produces a long non-coding RNA that regulates the reprogramming of pluripotent stem cells. This RNA suppresses induction of tumor protein p53 after DNA damage. It is thought to act as a sponge for microRNAs that regulate stem cell factors POU class 5 homeobox 1, Nanog, and SRY-box 2. This RNA may also have a extracellular role in modulating response to hypoxia in hepatocellular cancer cells. Expression of this transcript is associated with tumor progression and epithelial to mesenchymal transition and metastasis. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC-ROR	NR_152602.1	n.411-3542C>T		intron_variant, non_coding_transcript_variant
LINC-ROR	NR_048536.2	n.411-2228C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC-ROR	ENST00000553704.3	n.411-2228C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39251 AN: 151970 Hom.: 6361 Cov.: 33

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.258 AC: 39243 AN: 152088 Hom.: 6364 Cov.: 33 AF XY: 0.254 AC XY: 18877 AN XY: 74332

Gnomad4 AFR AF: 0.0837

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.274

Alfa AF: 0.310 Hom.: 1854

Bravo AF: 0.238

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	21
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs732982; hg19: chr18-54727459;