ENST00000706294.2:n.182+36430G>A

Variant names:

• chr6-131938581-G-A
• rs12529636
• ENST00000706294.2:n.182+36430G>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+36430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 152,294 control chromosomes in the GnomAD database, including 977 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 0.091 (977 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 2 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=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+27626G>A		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+34347G>A		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+14511G>A		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+34347G>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+36430G>A		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+36430G>A		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+34347G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0907 AC: 13809 AN: 152176 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0906 AC: 13800 AN: 152294 Hom.: 977 Cov.: 32 AF XY: 0.0961 AC XY: 7156 AN XY: 74468

African (AFR) AF: 0.0172 AC: 715 AN: 41580

American (AMR) AF: 0.110 AC: 1676 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1260 AN: 5166

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1090 AN: 10612

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.0940 AC: 6393 AN: 68018

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.107 Hom.: 448

Bravo AF: 0.0859

Asia WGS AF: 0.245 AC: 851 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.66
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs12529636; hg19: chr6-132259721;