rs9604529

Variant summary

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

The NR_164112.1(LINC00452):​n.1111A>G 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 0.192 in 1,289,082 control chromosomes in the GnomAD database, including 26,097 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 0.24 ( 5131 hom., cov: 33)
Exomes 𝑓: 0.19 ( 20966 hom. )

Consequence

LINC00452
NR_164112.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.299
Variant links:
Genes affected
LINC00452 (HGNC:42800): (long intergenic non-protein coding RNA 452)

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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC00452NR_164112.1 linkuse as main transcriptn.1111A>G non_coding_transcript_exon_variant 6/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC00452ENST00000609661.5 linkuse as main transcriptn.801A>G non_coding_transcript_exon_variant 5/85
LINC00452ENST00000426859.1 linkuse as main transcriptn.1111A>G non_coding_transcript_exon_variant 6/82
LINC00452ENST00000671032.1 linkuse as main transcriptn.433A>G non_coding_transcript_exon_variant 3/4

Frequencies

GnomAD3 genomes
AF:
0.235
AC:
35755
AN:
151952
Hom.:
5104
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.396
Gnomad AMI
AF:
0.412
Gnomad AMR
AF:
0.189
Gnomad ASJ
AF:
0.238
Gnomad EAS
AF:
0.0495
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.102
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.190
Gnomad OTH
AF:
0.234
GnomAD3 exomes
AF:
0.166
AC:
22294
AN:
134502
Hom.:
2274
AF XY:
0.162
AC XY:
11875
AN XY:
73238
show subpopulations
Gnomad AFR exome
AF:
0.404
Gnomad AMR exome
AF:
0.141
Gnomad ASJ exome
AF:
0.228
Gnomad EAS exome
AF:
0.0514
Gnomad SAS exome
AF:
0.102
Gnomad FIN exome
AF:
0.106
Gnomad NFE exome
AF:
0.193
Gnomad OTH exome
AF:
0.181
GnomAD4 exome
AF:
0.186
AC:
211075
AN:
1137012
Hom.:
20966
Cov.:
32
AF XY:
0.182
AC XY:
101605
AN XY:
557718
show subpopulations
Gnomad4 AFR exome
AF:
0.407
Gnomad4 AMR exome
AF:
0.143
Gnomad4 ASJ exome
AF:
0.230
Gnomad4 EAS exome
AF:
0.0512
Gnomad4 SAS exome
AF:
0.102
Gnomad4 FIN exome
AF:
0.117
Gnomad4 NFE exome
AF:
0.190
Gnomad4 OTH exome
AF:
0.192
GnomAD4 genome
AF:
0.236
AC:
35839
AN:
152070
Hom.:
5131
Cov.:
33
AF XY:
0.228
AC XY:
16920
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.397
Gnomad4 AMR
AF:
0.189
Gnomad4 ASJ
AF:
0.238
Gnomad4 EAS
AF:
0.0494
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.102
Gnomad4 NFE
AF:
0.190
Gnomad4 OTH
AF:
0.232
Alfa
AF:
0.195
Hom.:
5295
Bravo
AF:
0.253
Asia WGS
AF:
0.0870
AC:
305
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
2.3
DANN
Benign
0.34

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: rs9604529; hg19: chr13-114622597; API