rs12206863

Variant names:

• chr6-131947902-A-C
• rs12206863
• ENST00000706294.2:n.182+45751A>C

Variant summary

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

The ENST00000706294.2(LINC01013):​n.182+45751A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,252 control chromosomes in the GnomAD database, including 985 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 0.11 (985 hom., cov: 33)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.321
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+36947A>C		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+43668A>C		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+23832A>C		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+43668A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.2	n.182+45751A>C		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+45751A>C		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+43668A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16519 AN: 152134 Hom.: 986 Cov.: 33

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.0410

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.109 AC: 16527 AN: 152252 Hom.: 985 Cov.: 33 AF XY: 0.105 AC XY: 7834 AN XY: 74444

African (AFR) AF: 0.0739 AC: 3069 AN: 41554

American (AMR) AF: 0.121 AC: 1853 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3466

East Asian (EAS) AF: 0.0696 AC: 361 AN: 5190

South Asian (SAS) AF: 0.0419 AC: 202 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1297 AN: 10610

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8950 AN: 68002

Other (OTH) AF: 0.116 AC: 245 AN: 2108

Alfa AF: 0.111 Hom.: 361

Bravo AF: 0.108

Asia WGS AF: 0.0620 AC: 215 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs12206863; hg19: chr6-132269042;