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

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. 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

Publications

1 publications found

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:

ENSG00000301212 (HGNC:):

ENSG00000301212 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Gene	Transcript	HGVSc	Effect	Exon Rank
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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
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:

AN:

150448

Hom.:

Cov.:

show subpopulations

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

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

African (AFR)

AF:

0.00483

AC:

AN:

7046

American (AMR)

AF:

0.00

AC:

AN:

7412

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9214

East Asian (EAS)

AF:

0.00

AC:

AN:

22828

South Asian (SAS)

AF:

0.00109

AC:

AN:

2742

European-Finnish (FIN)

AF:

0.00

AC:

AN:

36606

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1292

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

157774

Other (OTH)

AF:

0.000304

AC:

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.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.258

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

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

African (AFR)

AF:

0.00207

AC:

AN:

40506

American (AMR)

AF:

0.000264

AC:

AN:

15154

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3462

East Asian (EAS)

AF:

0.00

AC:

AN:

5126

South Asian (SAS)

AF:

0.00

AC:

AN:

4760

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10502

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.0000148

AC:

AN:

67768

Other (OTH)

AF:

0.000480

AC:

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.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.256

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00169

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=99/1

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over