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GeneBe

rs9287022

Variant summary

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

The ENST00000666388.1(LINC02814):n.338-49314G>T 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 0.172 in 152,138 control chromosomes in the GnomAD database, including 3,843 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 0.17 ( 3843 hom., cov: 32)

Consequence

LINC02814
ENST00000666388.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212
Variant links:
Genes affected
LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02815XR_002958488.1 linkuse as main transcriptn.416-39727G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC02814ENST00000666388.1 linkuse as main transcriptn.338-49314G>T intron_variant, non_coding_transcript_variant
LINC02814ENST00000662083.1 linkuse as main transcriptn.46+41448G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.172
AC:
26140
AN:
152018
Hom.:
3836
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.399
Gnomad AMI
AF:
0.132
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.135
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.173
Gnomad FIN
AF:
0.0410
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.0626
Gnomad OTH
AF:
0.137
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.172
AC:
26178
AN:
152138
Hom.:
3843
Cov.:
32
AF XY:
0.171
AC XY:
12712
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.399
Gnomad4 AMR
AF:
0.151
Gnomad4 ASJ
AF:
0.135
Gnomad4 EAS
AF:
0.178
Gnomad4 SAS
AF:
0.173
Gnomad4 FIN
AF:
0.0410
Gnomad4 NFE
AF:
0.0626
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.0804
Hom.:
1307
Bravo
AF:
0.190
Asia WGS
AF:
0.169
AC:
588
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
4.4
Dann
Benign
0.72

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: rs9287022; hg19: chr1-229278349; API