5-17912590-A-T

Variant summary

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

The NR_134286.1(LINC02223):​n.579-7637A>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 0.447 in 151,924 control chromosomes in the GnomAD database, including 15,703 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 ( 15703 hom., cov: 32)

Consequence

LINC02223
NR_134286.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.601
Variant links:
Genes affected
LINC02223 (HGNC:53092): (long intergenic non-protein coding RNA 2223)

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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02223NR_134286.1 linkuse as main transcriptn.579-7637A>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02223ENST00000511596.5 linkuse as main transcriptn.196-7637A>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.447
AC:
67815
AN:
151806
Hom.:
15695
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.315
Gnomad AMI
AF:
0.495
Gnomad AMR
AF:
0.517
Gnomad ASJ
AF:
0.571
Gnomad EAS
AF:
0.492
Gnomad SAS
AF:
0.512
Gnomad FIN
AF:
0.434
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.497
Gnomad OTH
AF:
0.476
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.447
AC:
67841
AN:
151924
Hom.:
15703
Cov.:
32
AF XY:
0.445
AC XY:
33037
AN XY:
74272
show subpopulations
Gnomad4 AFR
AF:
0.314
Gnomad4 AMR
AF:
0.517
Gnomad4 ASJ
AF:
0.571
Gnomad4 EAS
AF:
0.492
Gnomad4 SAS
AF:
0.512
Gnomad4 FIN
AF:
0.434
Gnomad4 NFE
AF:
0.497
Gnomad4 OTH
AF:
0.477
Alfa
AF:
0.471
Hom.:
2155
Bravo
AF:
0.447
Asia WGS
AF:
0.496
AC:
1725
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.73
DANN
Benign
0.46

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: rs1443404; hg19: chr5-17912699; API