Variant rs2468574 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_187205.1(LINC02718):n.625-79739A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,878 control chromosomes in the GnomAD database, including 34,546 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 0.67 ( 34546 hom., cov: 32)

Consequence

LINC02718
NR_187205.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.752

Variant links:

Genes affected

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

LINC02718 links:

LOC124902646 (HGNC:):

LOC124902646 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LINC02718	NR_187205.1 link	n.625-79739A>C	intron_variant
LINC02718	NR_187206.1 link	n.625-80360A>C	intron_variant
LINC02718	NR_187207.1 link	n.625-80360A>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.666

AC:

101077

AN:

151760

Hom.:

34520

Cov.:

show subpopulations

Gnomad AFR

AF:

0.802

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.661

Gnomad ASJ

AF:

0.641

Gnomad EAS

AF:

0.772

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.568

Gnomad MID

AF:

0.713

Gnomad NFE

AF:

0.589

Gnomad OTH

AF:

0.655

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

GnomAD4 genome

AF:

0.666

AC:

101157

AN:

151878

Hom.:

34546

Cov.:

AF XY:

0.668

AC XY:

49574

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.801

Gnomad4 AMR

AF:

0.661

Gnomad4 ASJ

AF:

0.641

Gnomad4 EAS

AF:

0.772

Gnomad4 SAS

AF:

0.766

Gnomad4 FIN

AF:

0.568

Gnomad4 NFE

AF:

0.589

Gnomad4 OTH

AF:

0.658

Alfa

AF:

0.602

Hom.:

36267

Bravo

AF:

0.674

Asia WGS

AF:

0.776

AC:

2696

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.8

DANN

Benign

0.77

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