rs1045249

Variant names:

• chr2-87521282-G-T
• rs1045249
• ENST00000331944.10:n.293G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000331944.10(CYTOR):​n.293G>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. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.00060 (0 hom., cov: 24)
  • Exomes 𝑓: 0.00016 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CYTOR ENST00000331944.10 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524
• Publications: 1 publications found

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]

NCAL1 (HGNC:56663): (NK cell activity associated lncRNA 1)

ENSG00000301212 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000331944.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYTOR	NR_024204.2		n.605G>T		non_coding_transcript_exon	Exon 4 of 4
	CYTOR	NR_024205.3		n.441G>T		non_coding_transcript_exon	Exon 3 of 3
	CYTOR	NR_024206.2		n.295G>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYTOR	ENST00000331944.10	TSL:1	n.293G>T		non_coding_transcript_exon	Exon 2 of 2
	CYTOR	ENST00000413202.1	TSL:1	n.190G>T		non_coding_transcript_exon	Exon 2 of 2
	CYTOR	ENST00000414584.1	TSL:1	n.536G>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.000598 AC: 90 AN: 150448 Hom.: 0 Cov.: 24

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00483 AC: 34 AN: 7046

American (AMR) AF: 0.00 AC: 0 AN: 7412

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9214

East Asian (EAS) AF: 0.00 AC: 0 AN: 22828

South Asian (SAS) AF: 0.00109 AC: 3 AN: 2742

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 36606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 157774

Other (OTH) AF: 0.000304 AC: 5 AN: 16430

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00207 AC: 84 AN: 40506

American (AMR) AF: 0.000264 AC: 4 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5126

South Asian (SAS) AF: 0.00 AC: 0 AN: 4760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10502

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000148 AC: 1 AN: 67768

Other (OTH) AF: 0.000480 AC: 1 AN: 2082

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00169 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	16
DANN	Benign	0.91
PhyloP100		0.52
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=99/1	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1045249;

hg19: chr2-87820801;