GeneBe

6-131941221-C-T

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NR_187593.1(CCN2-AS1):​n.371+30266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)

Consequence

CCN2-AS1
NR_187593.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305
Variant links:
Genes affected
LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)
CCN2-AS1 (HGNC:40164): (CCN2 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCN2-AS1NR_187593.1 linkn.371+30266C>T intron_variant Intron 2 of 2
CCN2-AS1NR_187594.1 linkn.488+36987C>T intron_variant Intron 2 of 3
CCN2-AS1NR_187595.1 linkn.327+17151C>T intron_variant Intron 2 of 5
CCN2-AS1NR_187596.1 linkn.488+36987C>T intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC01013ENST00000706294.1 linkn.182+39070C>T intron_variant Intron 1 of 3
LINC01013ENST00000706326.1 linkn.239+39070C>T intron_variant Intron 1 of 2
LINC01013ENST00000706327.1 linkn.559+36987C>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
Cov.:
30
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.3
DANN
Benign
0.78

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-132262361; API