rs6791599

Variant summary

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

The NR_151704.1(LINC02009):​n.2100C>T 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 0.185 in 152,042 control chromosomes in the GnomAD database, including 3,313 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 0.18 ( 3313 hom., cov: 32)
Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

LINC02009
NR_151704.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.575
Variant links:
Genes affected
LINC02009 (HGNC:52845): (long intergenic non-protein coding RNA 2009)

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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02009NR_151704.1 linkuse as main transcriptn.2100C>T non_coding_transcript_exon_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC02009ENST00000635852.1 linkuse as main transcriptn.2024C>T non_coding_transcript_exon_variant 5/53
LINC02009ENST00000661642.1 linkuse as main transcriptn.1890C>T non_coding_transcript_exon_variant 4/4

Frequencies

GnomAD3 genomes
AF:
0.185
AC:
28036
AN:
151922
Hom.:
3307
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.333
Gnomad AMI
AF:
0.202
Gnomad AMR
AF:
0.105
Gnomad ASJ
AF:
0.151
Gnomad EAS
AF:
0.000770
Gnomad SAS
AF:
0.0214
Gnomad FIN
AF:
0.152
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.139
GnomAD4 exome
AF:
0.500
AC:
1
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 NFE exome
AF:
0.500
GnomAD4 genome
AF:
0.185
AC:
28079
AN:
152040
Hom.:
3313
Cov.:
32
AF XY:
0.179
AC XY:
13271
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.333
Gnomad4 AMR
AF:
0.105
Gnomad4 ASJ
AF:
0.151
Gnomad4 EAS
AF:
0.000772
Gnomad4 SAS
AF:
0.0218
Gnomad4 FIN
AF:
0.152
Gnomad4 NFE
AF:
0.146
Gnomad4 OTH
AF:
0.138
Alfa
AF:
0.173
Hom.:
364
Bravo
AF:
0.189
Asia WGS
AF:
0.0420
AC:
146
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.9
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.

Other links and lift over

dbSNP: rs6791599; hg19: chr3-46458942; API