rs1045249

chr2-87521282-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_024205.3(CYTOR):n.441G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.00060 (0 hom., cov: 24)
  • Exomes 𝑓: 0.00016 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CYTOR NR_024205.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524

Genes affected

CYTOR (HGNC:28717): (cytoskeleton regulator RNA) This gene produces a long non-coding RNA that is overexpressed in cancer cells and promotes cell proliferation and epithelial-mesenchymal transition. This RNA may bind enhancer of zeste homolog 2 and participate in the transcriptional silencing of tumor suppressor genes. It may act as a sponge for microRNAs. Alternatively spliced variants have been observed. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYTOR	NR_024205.3	n.441G>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYTOR	ENST00000646636.1	n.295+50978G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 90 AN: 150448 Hom.: 0 Cov.: 24 FAILED QC

Gnomad AFR AF: 0.00208

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000264

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000148

Gnomad OTH AF: 0.000485

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000161 AC: 42 AN: 261344 Hom.: 0 Cov.: 0 AF XY: 0.000129 AC XY: 17 AN XY: 131938

Gnomad4 AFR exome AF: 0.00483

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00109

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.000304

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000598 AC: 90 AN: 150562 Hom.: 0 Cov.: 24 AF XY: 0.000585 AC XY: 43 AN XY: 73562

Gnomad4 AFR AF: 0.00207

Gnomad4 AMR AF: 0.000264

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000148

Gnomad4 OTH AF: 0.000480

Alfa AF: 0.00169 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	16
Dann	Benign	0.91
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1045249; hg19: chr2-87820801;