rs12527705

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_187593.1(CCN2-AS1):​n.371+31156A>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

CCN2-AS1
NR_187593.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.545

Publications

2 publications found
Variant links:
Genes affected
LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)
CCN2-AS1 (HGNC:40164): (CCN2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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-AS1NR_187593.1 linkn.371+31156A>T intron_variant Intron 2 of 2
CCN2-AS1NR_187594.1 linkn.488+37877A>T intron_variant Intron 2 of 3
CCN2-AS1NR_187595.1 linkn.327+18041A>T intron_variant Intron 2 of 5
CCN2-AS1NR_187596.1 linkn.488+37877A>T intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01013ENST00000706294.2 linkn.182+39960A>T intron_variant Intron 1 of 3
LINC01013ENST00000706326.1 linkn.239+39960A>T intron_variant Intron 1 of 2
LINC01013ENST00000706327.1 linkn.559+37877A>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.0927
AC:
14109
AN:
152134
Hom.:
952
Cov.:
32
show subpopulations
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
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
632
1264
1897
2529
3161
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
184
368
552
736
920
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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

Publications

Other links and lift over

dbSNP: rs12527705; hg19: chr6-132263251; API