rs9399005

Variant names:

• chr6-131947824-C-T
• rs9399005
• ENST00000706294.2:n.182+45673C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 25 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187593.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCN2-AS1	NR_187593.1		n.371+36869C>T		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+43590C>T		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+23754C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000706294.2		n.182+45673C>T		intron	N/A
	LINC01013	ENST00000706326.1		n.239+45673C>T		intron	N/A
	LINC01013	ENST00000706327.1		n.559+43590C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34374 AN: 152034 Hom.: 4399 Cov.: 33

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.: 33 AF XY: 0.227 AC XY: 16870 AN XY: 74366

African (AFR) AF: 0.110 AC: 4557 AN: 41534

American (AMR) AF: 0.253 AC: 3872 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 661 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2256 AN: 5158

South Asian (SAS) AF: 0.320 AC: 1541 AN: 4818

European-Finnish (FIN) AF: 0.220 AC: 2324 AN: 10556

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18287 AN: 67994

Other (OTH) AF: 0.241 AC: 509 AN: 2114

Alfa AF: 0.261 Hom.: 11318

Bravo AF: 0.226

Asia WGS AF: 0.383 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.79
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9399005; hg19: chr6-132268964; COSMIC: COSV63466585;