rs6983267

Variant summary

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

The NR_109834(CCAT2):n.662G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.382 in 152022 control chromosomes in the gnomAD Genomes database, including 13511 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 ( 13511 hom., cov: 33)

Consequence

CCAT2
NR_109834 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.38

Links

CCAT2 (HGNC:47044):

CASC8 (HGNC:45129):

POU5F1B (HGNC:9223):

PCAT1 (HGNC:43022):

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

GnomAd 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
CCAT2	NR_109834.1 linkuse as main transcript	n.662G>T		non_coding_transcript_exon_variant	1/1
CASC8	NR_117100.1 linkuse as main transcript	n.1176+19769C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCAT2	ENST00000630920.1 linkuse as main transcript	n.662G>T		non_coding_transcript_exon_variant	1/1
CASC8	ENST00000502082.5 linkuse as main transcript	n.1176+19769C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.382

AC:

58042

AN:

152022

Hom.:

13511

Cov.:

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:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.00

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

Dann

Benign

0.86

Splicing

Find out SpliceAI 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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over