ENST00000706294.2:n.182+29650G>A

Variant names:

• chr6-131931801-G-A
• rs9321314
• ENST00000706294.2:n.182+29650G>A

Variant summary

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

The ENST00000706294.2(LINC01013):​n.182+29650G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,078 control chromosomes in the GnomAD database, including 3,365 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 0.19 (3365 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 4 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=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+20846G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+27567G>A		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+7731G>A		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+27567G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.2	n.182+29650G>A		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+29650G>A		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+27567G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29004 AN: 151960 Hom.: 3370 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.191 AC: 29004 AN: 152078 Hom.: 3365 Cov.: 32 AF XY: 0.199 AC XY: 14758 AN XY: 74318

African (AFR) AF: 0.122 AC: 5082 AN: 41488

American (AMR) AF: 0.181 AC: 2757 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1769 AN: 5158

South Asian (SAS) AF: 0.496 AC: 2382 AN: 4806

European-Finnish (FIN) AF: 0.210 AC: 2221 AN: 10570

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12732 AN: 67990

Other (OTH) AF: 0.210 AC: 443 AN: 2114

Alfa AF: 0.171 Hom.: 1298

Bravo AF: 0.180

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.3
DANN	Benign	0.62
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs9321314; hg19: chr6-132252941;