Variant 15-97396008-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000658446.1(LINC02254):n.639A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,092 control chromosomes in the GnomAD database, including 4,165 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 0.23 ( 4165 hom., cov: 32)

Consequence

LINC02254
ENST00000658446.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Variant links:

Genes affected

LINC02254 (HGNC:):

LINC02254 links:

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

LINC02253 links:

LINC02254 (HGNC:53152): (long intergenic non-protein coding RNA 2254)

LINC02254 links:

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LINC02254	NR_120324.1 link	n.755+1649A>G	intron_variant
LINC02253	NR_183853.1 link	n.293-15184T>C	intron_variant
LINC02253	NR_183854.1 link	n.293-15184T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC02254	ENST00000558621.2 link	n.755+1649A>G	intron_variant		1
LINC02254	ENST00000658446.1 link	n.639A>G	non_coding_transcript_exon_variant	5/5
LINC02253	ENST00000559321.2 link	n.251-15184T>C	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35193

AN:

151974

Hom.:

4160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.231

AC:

35203

AN:

152092

Hom.:

4165

Cov.:

AF XY:

0.230

AC XY:

17135

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.204

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.209

Gnomad4 EAS

AF:

0.106

Gnomad4 SAS

AF:

0.171

Gnomad4 FIN

AF:

0.271

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.240

Alfa

AF:

0.249

Hom.:

6417

Bravo

AF:

0.229

Asia WGS

AF:

0.125

AC:

435

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.14

DANN

Benign

0.51

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over