Variant rs10826519 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_120652.1(LINC01517):n.198-4370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,176 control chromosomes in the GnomAD database, including 17,448 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 0.44 ( 17427 hom., cov: 32)

Exomes 𝑓: 0.59 ( 21 hom. )

Consequence

LINC01517
NR_120652.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.648

Variant links:

Genes affected

LINC01517 (HGNC:51212): (long intergenic non-protein coding RNA 1517)

LINC01517 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01517	NR_120652.1 link	n.198-4370G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01517	ENST00000426922.6 link	n.290-110G>A	intron_variant	5
LINC01517	ENST00000616194.4 link	n.425-110G>A	intron_variant	5
LINC01517	ENST00000621861.1 link	n.631-4370G>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

67061

AN:

151942

Hom.:

17428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.540

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.573

Gnomad EAS

AF:

0.618

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.478

GnomAD4 exome

AF:

0.586

AC:

AN:

116

Hom.:

AF XY:

0.598

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.563

Gnomad4 NFE exome

AF:

0.593

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.441

AC:

67060

AN:

152060

Hom.:

17427

Cov.:

AF XY:

0.443

AC XY:

32894

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.465

Gnomad4 ASJ

AF:

0.573

Gnomad4 EAS

AF:

0.619

Gnomad4 SAS

AF:

0.525

Gnomad4 FIN

AF:

0.515

Gnomad4 NFE

AF:

0.576

Gnomad4 OTH

AF:

0.476

Alfa

AF:

0.512

Hom.:

5245

Bravo

AF:

0.423

Asia WGS

AF:

0.552

AC:

1920

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.34

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