GeneBe

rs3037970

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000435287.2(LINC01013):​n.309+2799_309+2803dupTAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22555 hom., cov: 0)

Consequence

LINC01013
ENST00000435287.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0280
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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+43098_371+43102dupTAAAA intron_variant
CCN2-AS1NR_187594.1 linkuse as main transcriptn.488+49819_488+49823dupTAAAA intron_variant
CCN2-AS1NR_187595.1 linkuse as main transcriptn.327+29983_327+29987dupTAAAA intron_variant
CCN2-AS1NR_187596.1 linkuse as main transcriptn.488+49819_488+49823dupTAAAA intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01013ENST00000435287.2 linkuse as main transcriptn.309+2799_309+2803dupTAAAA intron_variant 2
LINC01013ENST00000706294.1 linkuse as main transcriptn.182+51902_182+51906dupTAAAA intron_variant
LINC01013ENST00000706326.1 linkuse as main transcriptn.239+51902_239+51906dupTAAAA intron_variant

Frequencies

GnomAD3 genomes
AF:
0.538
AC:
81270
AN:
151176
Hom.:
22512
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.695
Gnomad AMI
AF:
0.564
Gnomad AMR
AF:
0.485
Gnomad ASJ
AF:
0.396
Gnomad EAS
AF:
0.522
Gnomad SAS
AF:
0.497
Gnomad FIN
AF:
0.463
Gnomad MID
AF:
0.558
Gnomad NFE
AF:
0.477
Gnomad OTH
AF:
0.526
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.538
AC:
81367
AN:
151296
Hom.:
22555
Cov.:
0
AF XY:
0.535
AC XY:
39540
AN XY:
73896
show subpopulations
Gnomad4 AFR
AF:
0.695
Gnomad4 AMR
AF:
0.485
Gnomad4 ASJ
AF:
0.396
Gnomad4 EAS
AF:
0.522
Gnomad4 SAS
AF:
0.498
Gnomad4 FIN
AF:
0.463
Gnomad4 NFE
AF:
0.477
Gnomad4 OTH
AF:
0.529
Alfa
AF:
0.528
Hom.:
1666
Asia WGS
AF:
0.560
AC:
1944
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs3037970; hg19: chr6-132275192; API