rs12526196

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.139
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

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-AS1NR_187593.1 linkuse as main transcriptn.371+31381T>C intron_variant
CCN2-AS1NR_187594.1 linkuse as main transcriptn.488+38102T>C intron_variant
CCN2-AS1NR_187595.1 linkuse as main transcriptn.327+18266T>C intron_variant
CCN2-AS1NR_187596.1 linkuse as main transcriptn.488+38102T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01013ENST00000706294.1 linkuse as main transcriptn.182+40185T>C intron_variant
LINC01013ENST00000706326.1 linkuse as main transcriptn.239+40185T>C intron_variant
LINC01013ENST00000706327.1 linkuse as main transcriptn.559+38102T>C intron_variant

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12526196; hg19: chr6-132263476; API