Variant rs9399005 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_187593.1(CCN2-AS1):n.371+36869C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,152 control chromosomes in the GnomAD database, including 4,406 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 0.23 ( 4406 hom., cov: 33)

Consequence

CCN2-AS1
NR_187593.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Variant links:

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

LINC01013 links:

CCN2-AS1 (HGNC:40164): (CCN2 antisense RNA 1)

CCN2-AS1 links:

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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
CCN2-AS1	NR_187593.1 link	n.371+36869C>T	intron_variant
CCN2-AS1	NR_187594.1 link	n.488+43590C>T	intron_variant
CCN2-AS1	NR_187595.1 link	n.327+23754C>T	intron_variant
CCN2-AS1	NR_187596.1 link	n.488+43590C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
LINC01013	ENST00000706294.1 link	n.182+45673C>T	intron_variant
LINC01013	ENST00000706326.1 link	n.239+45673C>T	intron_variant
LINC01013	ENST00000706327.1 link	n.559+43590C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34374

AN:

152034

Hom.:

4399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.350

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.220

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.238

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.226

AC:

34399

AN:

152152

Hom.:

4406

Cov.:

AF XY:

0.227

AC XY:

16870

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.190

Gnomad4 EAS

AF:

0.437

Gnomad4 SAS

AF:

0.320

Gnomad4 FIN

AF:

0.220

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.240

Hom.:

444

Bravo

AF:

0.226

Asia WGS

AF:

0.383

AC:

1328

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.0

DANN

Benign

0.79

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