rs912343

Variant summary

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

The NR_146552.1(LINC02299):​n.130+3511A>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 0.187 in 152,234 control chromosomes in the GnomAD database, including 2,737 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 0.19 ( 2737 hom., cov: 33)

Consequence

LINC02299
NR_146552.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.998
Variant links:
Genes affected
LINC02299 (HGNC:53218): (long intergenic non-protein coding RNA 2299)

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 (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02299NR_146552.1 linkuse as main transcriptn.130+3511A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC02299ENST00000650059.1 linkuse as main transcriptn.159+3511A>G intron_variant, non_coding_transcript_variant
LINC02299ENST00000556669.1 linkuse as main transcriptn.130+3511A>G intron_variant, non_coding_transcript_variant 5
LINC02299ENST00000654843.1 linkuse as main transcriptn.140+3511A>G intron_variant, non_coding_transcript_variant
LINC02299ENST00000664687.1 linkuse as main transcriptn.131+3511A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.187
AC:
28473
AN:
152116
Hom.:
2737
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.218
Gnomad AMI
AF:
0.104
Gnomad AMR
AF:
0.127
Gnomad ASJ
AF:
0.206
Gnomad EAS
AF:
0.127
Gnomad SAS
AF:
0.253
Gnomad FIN
AF:
0.199
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.180
Gnomad OTH
AF:
0.185
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.187
AC:
28481
AN:
152234
Hom.:
2737
Cov.:
33
AF XY:
0.189
AC XY:
14053
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.218
Gnomad4 AMR
AF:
0.126
Gnomad4 ASJ
AF:
0.206
Gnomad4 EAS
AF:
0.128
Gnomad4 SAS
AF:
0.254
Gnomad4 FIN
AF:
0.199
Gnomad4 NFE
AF:
0.180
Gnomad4 OTH
AF:
0.183
Alfa
AF:
0.181
Hom.:
3892
Bravo
AF:
0.179
Asia WGS
AF:
0.202
AC:
702
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
0.30
DANN
Benign
0.47

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: rs912343; hg19: chr14-97214117; API