rs996297

Variant summary

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

The NR_046989.1(LINC00351):​n.493+69267A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,096 control chromosomes in the GnomAD database, including 38,932 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 0.71 ( 38932 hom., cov: 33)

Consequence

LINC00351
NR_046989.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.904
Variant links:
Genes affected
LINC00351 (HGNC:42669): (long intergenic non-protein coding RNA 351)

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC00351NR_046989.1 linkuse as main transcriptn.493+69267A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC00351ENST00000424926.2 linkuse as main transcriptn.495+69267A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.709
AC:
107692
AN:
151980
Hom.:
38891
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.844
Gnomad AMI
AF:
0.620
Gnomad AMR
AF:
0.684
Gnomad ASJ
AF:
0.475
Gnomad EAS
AF:
0.561
Gnomad SAS
AF:
0.540
Gnomad FIN
AF:
0.652
Gnomad MID
AF:
0.627
Gnomad NFE
AF:
0.678
Gnomad OTH
AF:
0.677
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.709
AC:
107780
AN:
152096
Hom.:
38932
Cov.:
33
AF XY:
0.702
AC XY:
52169
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.844
Gnomad4 AMR
AF:
0.684
Gnomad4 ASJ
AF:
0.475
Gnomad4 EAS
AF:
0.561
Gnomad4 SAS
AF:
0.539
Gnomad4 FIN
AF:
0.652
Gnomad4 NFE
AF:
0.678
Gnomad4 OTH
AF:
0.672
Alfa
AF:
0.704
Hom.:
4704
Bravo
AF:
0.716
Asia WGS
AF:
0.565
AC:
1967
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.087
DANN
Benign
0.30

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: rs996297; hg19: chr13-86007497; API