Menu
GeneBe

rs6983267

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_109834.1(CCAT2):n.662G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.382 in 152,144 control chromosomes in the GnomAD database, including 13,516 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 0.38 ( 13516 hom., cov: 33)
Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

CCAT2
NR_109834.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.38
Variant links:
Genes affected
CCAT2 (HGNC:47044): (colon cancer associated transcript 2) This gene produces a long non-coding RNA that is upregulated in colon cancer and other cancers. This transcript promotes cell proliferation and suppresses apoptosis. It negatively regulates the biogenesis of microRNA 145. [provided by RefSeq, Dec 2017]
CASC8 (HGNC:45129): (cancer susceptibility 8)
POU5F1B (HGNC:9223): (POU class 5 homeobox 1B) This intronless gene was thought to be a transcribed pseudogene of POU class 5 homeobox 1, however, it has been reported that this gene can encode a functional protein. The encoded protein is nearly the same length as and highly similar to the POU class 5 homeobox 1 transcription factor, has been shown to be a weak transcriptional activator and may play a role in carcinogenesis and eye development. [provided by RefSeq, Apr 2009]
PCAT1 (HGNC:43022): (prostate cancer associated transcript 1) This gene produces a long non-coding RNA that promotes cell proliferation and is upregulated in prostate, colorectal, and other cancers. This RNA negatively regulates the BRCA2 tumor suppressor protein and positively regulates Myc oncoprotein. It contains binding sites for microRNAs, and may act as a sponge for microRNAs that regulate cell growth pathways. [provided by RefSeq, Dec 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCAT2NR_109834.1 linkuse as main transcriptn.662G>T non_coding_transcript_exon_variant 1/1
CASC8NR_117100.1 linkuse as main transcriptn.1176+19769C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCAT2ENST00000630920.1 linkuse as main transcriptn.662G>T non_coding_transcript_exon_variant 1/1
CASC8ENST00000502082.5 linkuse as main transcriptn.1176+19769C>A intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.382
AC:
58042
AN:
152022
Hom.:
13511
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.105
Gnomad AMI
AF:
0.363
Gnomad AMR
AF:
0.442
Gnomad ASJ
AF:
0.506
Gnomad EAS
AF:
0.602
Gnomad SAS
AF:
0.495
Gnomad FIN
AF:
0.474
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.491
Gnomad OTH
AF:
0.418
GnomAD4 exome
AF:
0.250
AC:
1
AN:
4
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 NFE exome
AF:
0.500
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.382
AC:
58042
AN:
152140
Hom.:
13516
Cov.:
33
AF XY:
0.386
AC XY:
28736
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.104
Gnomad4 AMR
AF:
0.442
Gnomad4 ASJ
AF:
0.506
Gnomad4 EAS
AF:
0.601
Gnomad4 SAS
AF:
0.495
Gnomad4 FIN
AF:
0.474
Gnomad4 NFE
AF:
0.491
Gnomad4 OTH
AF:
0.423
Alfa
AF:
0.475
Hom.:
40970
Bravo
AF:
0.364
Asia WGS
AF:
0.503
AC:
1750
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
Cadd
Benign
18
Dann
Benign
0.86

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.

Other links and lift over

dbSNP: rs6983267; hg19: chr8-128413305; COSMIC: COSV72370033; COSMIC: COSV72370033; API