GeneBe

chr6-131958700-G-T

Position:

Variant summary

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

The ENST00000435287.2(LINC01013):​n.309+7446G>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: 32)

Consequence

LINC01013
ENST00000435287.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.52
Variant links:
Genes affected

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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=-0.78).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCN2-AS1NR_187593.1 linkuse as main transcriptn.371+47745G>T intron_variant
CCN2-AS1NR_187594.1 linkuse as main transcriptn.489-51157G>T intron_variant
CCN2-AS1NR_187595.1 linkuse as main transcriptn.327+34630G>T intron_variant
CCN2-AS1NR_187596.1 linkuse as main transcriptn.488+54466G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01013ENST00000435287.2 linkuse as main transcriptn.309+7446G>T intron_variant 2
LINC01013ENST00000706294.1 linkuse as main transcriptn.183-51157G>T intron_variant
LINC01013ENST00000706326.1 linkuse as main transcriptn.239+56549G>T intron_variant

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
9.6
DANN
Benign
0.69

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: chr6-132279840; API