14-53725754-C-T

Variant summary

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

The NR_184212.1(LINC02331):​n.767+24248G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,830 control chromosomes in the GnomAD database, including 46,609 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 ( 46609 hom., cov: 29)

Consequence

LINC02331
NR_184212.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.112
Variant links:
Genes affected
LINC02331 (HGNC:53251): (long intergenic non-protein coding RNA 2331)

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=-0.94).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02331NR_184212.1 linkuse as main transcriptn.767+24248G>A intron_variant
LINC02331NR_184213.1 linkuse as main transcriptn.768-22600G>A intron_variant
LINC02331NR_184214.1 linkuse as main transcriptn.778+24248G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02331ENST00000418927.2 linkuse as main transcriptn.842+24248G>A intron_variant 5
ENSG00000237356ENST00000648066.1 linkuse as main transcriptn.511-11913C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.783
AC:
118779
AN:
151712
Hom.:
46584
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.733
Gnomad AMI
AF:
0.843
Gnomad AMR
AF:
0.825
Gnomad ASJ
AF:
0.879
Gnomad EAS
AF:
0.807
Gnomad SAS
AF:
0.709
Gnomad FIN
AF:
0.807
Gnomad MID
AF:
0.826
Gnomad NFE
AF:
0.796
Gnomad OTH
AF:
0.816
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.783
AC:
118859
AN:
151830
Hom.:
46609
Cov.:
29
AF XY:
0.781
AC XY:
57989
AN XY:
74206
show subpopulations
Gnomad4 AFR
AF:
0.733
Gnomad4 AMR
AF:
0.825
Gnomad4 ASJ
AF:
0.879
Gnomad4 EAS
AF:
0.807
Gnomad4 SAS
AF:
0.709
Gnomad4 FIN
AF:
0.807
Gnomad4 NFE
AF:
0.796
Gnomad4 OTH
AF:
0.817
Alfa
AF:
0.800
Hom.:
69594
Bravo
AF:
0.786
Asia WGS
AF:
0.740
AC:
2577
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.3
DANN
Benign
0.61

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: rs210332; hg19: chr14-54192472; API