dbSNP rs1045249: CYTOR:n.293G>T (chr2-87521282-G-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -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. 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
ENST00000331944.10 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.524

Variant links:

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]

CYTOR links:

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

NCAL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	Exon rank
CYTOR	NR_024204.2 link	n.605G>T	non_coding_transcript_exon_variant	Exon 4 of 4
CYTOR	NR_024205.3 link	n.441G>T	non_coding_transcript_exon_variant	Exon 3 of 3
CYTOR	NR_024206.2 link	n.295G>T	non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CYTOR	ENST00000331944.10 link	n.293G>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
CYTOR	ENST00000413202.1 link	n.190G>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
CYTOR	ENST00000414584.1 link	n.536G>T	non_coding_transcript_exon_variant	Exon 4 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

150448

Hom.:

Cov.:

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:

AN:

261344

Hom.:

Cov.:

AF XY:

0.000129

AC XY:

AN XY:

131938

show subpopulations

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:

AN:

150562

Hom.:

Cov.:

AF XY:

0.000585

AC XY:

AN XY:

73562

show subpopulations

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.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over