rs12191459

Variant names:

• chr6-131946599-C-T
• rs12191459
• ENST00000706294.2:n.182+44448C>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+44448C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,150 control chromosomes in the GnomAD database, including 1,292 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 0.13 (1292 hom., cov: 33)
• Consequence: LINC01013 ENST00000706294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+35644C>T		intron_variant	Intron 2 of 2
CCN2-AS1	NR_187594.1	n.488+42365C>T		intron_variant	Intron 2 of 3
CCN2-AS1	NR_187595.1	n.327+22529C>T		intron_variant	Intron 2 of 5
CCN2-AS1	NR_187596.1	n.488+42365C>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+44448C>T		intron_variant	Intron 1 of 3
LINC01013	ENST00000706326.1	n.239+44448C>T		intron_variant	Intron 1 of 2
LINC01013	ENST00000706327.1	n.559+42365C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19094 AN: 152032 Hom.: 1292 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.126 AC: 19108 AN: 152150 Hom.: 1292 Cov.: 33 AF XY: 0.123 AC XY: 9118 AN XY: 74370

African (AFR) AF: 0.151 AC: 6278 AN: 41476

American (AMR) AF: 0.122 AC: 1871 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.0683 AC: 354 AN: 5184

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4820

European-Finnish (FIN) AF: 0.120 AC: 1269 AN: 10592

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8334 AN: 68022

Other (OTH) AF: 0.127 AC: 269 AN: 2110

Alfa AF: 0.123 Hom.: 540

Bravo AF: 0.128

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.49
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs12191459; hg19: chr6-132267739;