rs12098564

Variant summary

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

The NR_120667.1(LINC01519):​n.1897T>C 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 0.0711 in 152,206 control chromosomes in the GnomAD database, including 967 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 0.071 ( 967 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

LINC01519
NR_120667.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.332
Variant links:
Genes affected
LINC01519 (HGNC:51217): (long intergenic non-protein coding RNA 1519)

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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC01519NR_120667.1 linkuse as main transcriptn.1897T>C non_coding_transcript_exon_variant 4/4
LINC01519NR_120668.1 linkuse as main transcriptn.1050T>C non_coding_transcript_exon_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC01519ENST00000454178.1 linkuse as main transcriptn.1879T>C non_coding_transcript_exon_variant 3/35

Frequencies

GnomAD3 genomes
AF:
0.0710
AC:
10803
AN:
152086
Hom.:
969
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0508
Gnomad ASJ
AF:
0.00720
Gnomad EAS
AF:
0.0128
Gnomad SAS
AF:
0.0182
Gnomad FIN
AF:
0.0266
Gnomad MID
AF:
0.0570
Gnomad NFE
AF:
0.0150
Gnomad OTH
AF:
0.0569
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
6
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
6
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.0711
AC:
10825
AN:
152206
Hom.:
967
Cov.:
33
AF XY:
0.0701
AC XY:
5218
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.0509
Gnomad4 ASJ
AF:
0.00720
Gnomad4 EAS
AF:
0.0128
Gnomad4 SAS
AF:
0.0180
Gnomad4 FIN
AF:
0.0266
Gnomad4 NFE
AF:
0.0151
Gnomad4 OTH
AF:
0.0563
Alfa
AF:
0.0276
Hom.:
212
Bravo
AF:
0.0810
Asia WGS
AF:
0.0360
AC:
129
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.86
DANN
Benign
0.61

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: rs12098564; hg19: chr10-86953327; API