5-118437000-T-G

Variant summary

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

The NR_104610.1(LINC02208):​n.2657+31302A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,116 control chromosomes in the GnomAD database, including 47,226 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 0.78 ( 47226 hom., cov: 32)

Consequence

LINC02208
NR_104610.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38
Variant links:
Genes affected
LINC02208 (HGNC:52978): (long intergenic non-protein coding RNA 2208)

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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LINC02208NR_104610.1 linkn.2657+31302A>C intron_variant Intron 9 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02208ENST00000653787.1 linkn.685+37372A>C intron_variant Intron 5 of 5
LINC02208ENST00000654806.1 linkn.810+35063A>C intron_variant Intron 6 of 6
LINC02208ENST00000659234.1 linkn.890+35063A>C intron_variant Intron 8 of 8

Frequencies

GnomAD3 genomes
AF:
0.781
AC:
118652
AN:
151998
Hom.:
47194
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.632
Gnomad AMI
AF:
0.913
Gnomad AMR
AF:
0.860
Gnomad ASJ
AF:
0.889
Gnomad EAS
AF:
0.979
Gnomad SAS
AF:
0.902
Gnomad FIN
AF:
0.754
Gnomad MID
AF:
0.854
Gnomad NFE
AF:
0.826
Gnomad OTH
AF:
0.800
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.781
AC:
118731
AN:
152116
Hom.:
47226
Cov.:
32
AF XY:
0.781
AC XY:
58078
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.632
Gnomad4 AMR
AF:
0.860
Gnomad4 ASJ
AF:
0.889
Gnomad4 EAS
AF:
0.979
Gnomad4 SAS
AF:
0.901
Gnomad4 FIN
AF:
0.754
Gnomad4 NFE
AF:
0.826
Gnomad4 OTH
AF:
0.803
Alfa
AF:
0.820
Hom.:
55959
Bravo
AF:
0.782
Asia WGS
AF:
0.925
AC:
3212
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.21
DANN
Benign
0.40

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: rs7448017; hg19: chr5-117772695; API