10-16280711-A-G

Variant summary

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

The NR_184075.1(LINC02654):​n.693+1962A>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 0.454 in 152,164 control chromosomes in the GnomAD database, including 19,511 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 0.45 ( 19511 hom., cov: 32)

Consequence

LINC02654
NR_184075.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.854
Variant links:
Genes affected
LINC02654 (HGNC:54140): (long intergenic non-protein coding RNA 2654)

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 (NFE) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02654NR_184075.1 linkuse as main transcriptn.693+1962A>G intron_variant, non_coding_transcript_variant
LINC02654NR_184073.1 linkuse as main transcriptn.693+1962A>G intron_variant, non_coding_transcript_variant
LINC02654NR_184074.1 linkuse as main transcriptn.693+1962A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02654ENST00000652949.1 linkuse as main transcriptn.657+1962A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.455
AC:
69129
AN:
152046
Hom.:
19506
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.140
Gnomad AMI
AF:
0.553
Gnomad AMR
AF:
0.565
Gnomad ASJ
AF:
0.641
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.285
Gnomad FIN
AF:
0.652
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.617
Gnomad OTH
AF:
0.496
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.454
AC:
69134
AN:
152164
Hom.:
19511
Cov.:
32
AF XY:
0.452
AC XY:
33630
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.139
Gnomad4 AMR
AF:
0.565
Gnomad4 ASJ
AF:
0.641
Gnomad4 EAS
AF:
0.115
Gnomad4 SAS
AF:
0.284
Gnomad4 FIN
AF:
0.652
Gnomad4 NFE
AF:
0.617
Gnomad4 OTH
AF:
0.491
Alfa
AF:
0.588
Hom.:
26669
Bravo
AF:
0.440
Asia WGS
AF:
0.202
AC:
703
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.060
DANN
Benign
0.66

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: rs7075260; hg19: chr10-16322710; API