ENST00000706294.1:n.182+40185T>C

Variant names:

• chr6-131942336-T-C
• rs12526196
• ENST00000706294.2:n.182+40185T>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+40185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 152,258 control chromosomes in the GnomAD database, including 950 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 (950 hom., cov: 32)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 14 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706294.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCN2-AS1	NR_187593.1		n.371+31381T>C		intron	N/A
	CCN2-AS1	NR_187594.1		n.488+38102T>C		intron	N/A
	CCN2-AS1	NR_187595.1		n.327+18266T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01013	ENST00000706294.2		n.182+40185T>C		intron	N/A
	LINC01013	ENST00000706326.1		n.239+40185T>C		intron	N/A
	LINC01013	ENST00000706327.1		n.559+38102T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0927 AC: 14100 AN: 152140 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0926 AC: 14098 AN: 152258 Hom.: 950 Cov.: 32 AF XY: 0.0979 AC XY: 7287 AN XY: 74426

African (AFR) AF: 0.0182 AC: 757 AN: 41568

American (AMR) AF: 0.111 AC: 1691 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3470

East Asian (EAS) AF: 0.185 AC: 956 AN: 5172

South Asian (SAS) AF: 0.314 AC: 1516 AN: 4826

European-Finnish (FIN) AF: 0.102 AC: 1078 AN: 10600

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

European-Non Finnish (NFE) AF: 0.104 AC: 7081 AN: 68014

Other (OTH) AF: 0.110 AC: 231 AN: 2108

Alfa AF: 0.112 Hom.: 976

Bravo AF: 0.0874

Asia WGS AF: 0.227 AC: 788 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12526196; hg19: chr6-132263476;