ENST00000435287.2:n.310-34841A>G

Variant summary

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

The ENST00000435287.2(LINC01013):​n.310-34841A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,028 control chromosomes in the GnomAD database, including 35,316 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 0.67 ( 35316 hom., cov: 32)

Consequence

LINC01013
ENST00000435287.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCN2-AS1NR_187593.1 linkn.372-56564A>G intron_variant Intron 2 of 2
CCN2-AS1NR_187594.1 linkn.556+32443A>G intron_variant Intron 3 of 3
CCN2-AS1NR_187595.1 linkn.396-32426A>G intron_variant Intron 3 of 5
CCN2-AS1NR_187596.1 linkn.489-56564A>G intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01013ENST00000435287.2 linkn.310-34841A>G intron_variant Intron 1 of 1 2
LINC01013ENST00000706294.1 linkn.251-32426A>G intron_variant Intron 2 of 3
LINC01013ENST00000706295.1 linkn.154+32443A>G intron_variant Intron 3 of 6

Frequencies

GnomAD3 genomes
AF:
0.669
AC:
101597
AN:
151910
Hom.:
35274
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.868
Gnomad AMI
AF:
0.595
Gnomad AMR
AF:
0.536
Gnomad ASJ
AF:
0.548
Gnomad EAS
AF:
0.627
Gnomad SAS
AF:
0.613
Gnomad FIN
AF:
0.650
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.596
Gnomad OTH
AF:
0.647
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.669
AC:
101697
AN:
152028
Hom.:
35316
Cov.:
32
AF XY:
0.666
AC XY:
49483
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.868
Gnomad4 AMR
AF:
0.535
Gnomad4 ASJ
AF:
0.548
Gnomad4 EAS
AF:
0.627
Gnomad4 SAS
AF:
0.614
Gnomad4 FIN
AF:
0.650
Gnomad4 NFE
AF:
0.596
Gnomad4 OTH
AF:
0.650
Alfa
AF:
0.603
Hom.:
33818
Bravo
AF:
0.672
Asia WGS
AF:
0.666
AC:
2318
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.63
DANN
Benign
0.32

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: rs975515; hg19: chr6-132363507; API