rs10498284

Variant summary

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

The ENST00000546412.2(LINC02306):​n.537+16755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,960 control chromosomes in the GnomAD database, including 4,285 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 0.19 ( 4285 hom., cov: 32)

Consequence

LINC02306
ENST00000546412.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.497
Variant links:
Genes affected
LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02306ENST00000546412.2 linkn.537+16755C>T intron_variant Intron 5 of 9 3
LINC02306ENST00000657312.1 linkn.702+16790C>T intron_variant Intron 6 of 6

Frequencies

GnomAD3 genomes
AF:
0.186
AC:
28262
AN:
151842
Hom.:
4265
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.419
Gnomad AMI
AF:
0.0230
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.0971
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.200
Gnomad FIN
AF:
0.0813
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.0766
Gnomad OTH
AF:
0.159
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.186
AC:
28332
AN:
151960
Hom.:
4285
Cov.:
32
AF XY:
0.187
AC XY:
13854
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.419
Gnomad4 AMR
AF:
0.152
Gnomad4 ASJ
AF:
0.0971
Gnomad4 EAS
AF:
0.178
Gnomad4 SAS
AF:
0.199
Gnomad4 FIN
AF:
0.0813
Gnomad4 NFE
AF:
0.0766
Gnomad4 OTH
AF:
0.163
Alfa
AF:
0.144
Hom.:
641
Bravo
AF:
0.201
Asia WGS
AF:
0.214
AC:
745
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
7.4
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: rs10498284; hg19: chr14-26288301; API