ENST00000706294.2:n.182+39960A>T

Variant names:

• chr6-131942111-A-T
• rs12527705
• ENST00000706294.2:n.182+39960A>T

Variant summary

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

The ENST00000706294.2(LINC01013):​n.182+39960A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 152,252 control chromosomes in the GnomAD database, including 953 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 0.093 (953 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+31156A>T		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+37877A>T		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+18041A>T		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+37877A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.2	n.182+39960A>T		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+39960A>T		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+37877A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0927 AC: 14109 AN: 152134 Hom.: 952 Cov.: 32

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0927 AC: 14107 AN: 152252 Hom.: 953 Cov.: 32 AF XY: 0.0980 AC XY: 7297 AN XY: 74438

African (AFR) AF: 0.0183 AC: 762 AN: 41576

American (AMR) AF: 0.111 AC: 1692 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3472

East Asian (EAS) AF: 0.186 AC: 964 AN: 5184

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4826

European-Finnish (FIN) AF: 0.102 AC: 1082 AN: 10606

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7071 AN: 67984

Other (OTH) AF: 0.111 AC: 234 AN: 2114

Alfa AF: 0.102 Hom.: 129

Bravo AF: 0.0874

Asia WGS AF: 0.224 AC: 776 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.0
DANN	Benign	0.84
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs12527705; hg19: chr6-132263251;