rs12526196

Positions:

• chr6-131942336-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_187593.1(CCN2-AS1):​n.371+31381T>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: CCN2-AS1 NR_187593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

LINC01013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCN2-AS1	NR_187593.1	n.371+31381T>C		intron_variant
CCN2-AS1	NR_187594.1	n.488+38102T>C		intron_variant
CCN2-AS1	NR_187595.1	n.327+18266T>C		intron_variant
CCN2-AS1	NR_187596.1	n.488+38102T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01013	ENST00000706294.1	n.182+40185T>C		intron_variant
LINC01013	ENST00000706326.1	n.239+40185T>C		intron_variant
LINC01013	ENST00000706327.1	n.559+38102T>C		intron_variant

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

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.110

Alfa AF: 0.114 Hom.: 865

Bravo AF: 0.0874

Asia WGS AF: 0.227 AC: 788 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12526196; hg19: chr6-132263476;