ENST00000647635.1:n.159-1725C>T

Variant summary

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

The ENST00000647635.1(LINC02752):​n.159-1725C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,794 control chromosomes in the GnomAD database, including 8,726 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 0.32 ( 8726 hom., cov: 31)

Consequence

LINC02752
ENST00000647635.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.177
Variant links:
Genes affected
LINC02752 (HGNC:54272): (long intergenic non-protein coding RNA 2752)

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=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC02752NR_187401.1 linkn.97+630C>T intron_variant Intron 1 of 2
LINC02752NR_187402.1 linkn.97+630C>T intron_variant Intron 1 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02752ENST00000647635.1 linkn.159-1725C>T intron_variant Intron 1 of 6

Frequencies

GnomAD3 genomes
AF:
0.322
AC:
48850
AN:
151676
Hom.:
8736
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.479
Gnomad AMR
AF:
0.420
Gnomad ASJ
AF:
0.394
Gnomad EAS
AF:
0.314
Gnomad SAS
AF:
0.256
Gnomad FIN
AF:
0.298
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.393
Gnomad OTH
AF:
0.372
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.322
AC:
48850
AN:
151794
Hom.:
8726
Cov.:
31
AF XY:
0.319
AC XY:
23647
AN XY:
74180
show subpopulations
Gnomad4 AFR
AF:
0.172
Gnomad4 AMR
AF:
0.420
Gnomad4 ASJ
AF:
0.394
Gnomad4 EAS
AF:
0.314
Gnomad4 SAS
AF:
0.257
Gnomad4 FIN
AF:
0.298
Gnomad4 NFE
AF:
0.393
Gnomad4 OTH
AF:
0.370
Alfa
AF:
0.362
Hom.:
2133
Bravo
AF:
0.329
Asia WGS
AF:
0.279
AC:
970
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.2
DANN
Benign
0.62

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: rs12794717; hg19: chr11-11137658; API