rs9493149

Variant names:

• chr6-131937619-G-A
• rs9493149
• ENST00000706294.2:n.182+35468G>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+35468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,050 control chromosomes in the GnomAD database, including 3,494 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 (3494 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+26664G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+33385G>A		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+13549G>A		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+33385G>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+35468G>A		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+35468G>A		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+33385G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29615 AN: 151932 Hom.: 3497 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.195 AC: 29618 AN: 152050 Hom.: 3494 Cov.: 32 AF XY: 0.203 AC XY: 15062 AN XY: 74324

African (AFR) AF: 0.124 AC: 5134 AN: 41486

American (AMR) AF: 0.188 AC: 2869 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5160

South Asian (SAS) AF: 0.504 AC: 2425 AN: 4810

European-Finnish (FIN) AF: 0.209 AC: 2213 AN: 10564

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13118 AN: 67964

Other (OTH) AF: 0.219 AC: 463 AN: 2116

Alfa AF: 0.201 Hom.: 6090

Bravo AF: 0.185

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.62
DANN	Benign	0.37
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9493149; hg19: chr6-132258759;