rs17798800

Variant summary

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

The ENST00000605909.1(LINC02343):​n.82+28266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,056 control chromosomes in the GnomAD database, including 2,727 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 0.19 ( 2727 hom., cov: 32)

Consequence

LINC02343
ENST00000605909.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.479
Variant links:
Genes affected

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02343NR_146542.1 linkuse as main transcriptn.82+28266C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02343ENST00000605909.1 linkuse as main transcriptn.82+28266C>T intron_variant 4
LINC02343ENST00000664334.1 linkuse as main transcriptn.139+28266C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.185
AC:
28170
AN:
151936
Hom.:
2722
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.187
Gnomad AMI
AF:
0.207
Gnomad AMR
AF:
0.136
Gnomad ASJ
AF:
0.146
Gnomad EAS
AF:
0.138
Gnomad SAS
AF:
0.210
Gnomad FIN
AF:
0.200
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.198
Gnomad OTH
AF:
0.171
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.185
AC:
28180
AN:
152056
Hom.:
2727
Cov.:
32
AF XY:
0.185
AC XY:
13764
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.187
Gnomad4 AMR
AF:
0.136
Gnomad4 ASJ
AF:
0.146
Gnomad4 EAS
AF:
0.137
Gnomad4 SAS
AF:
0.210
Gnomad4 FIN
AF:
0.200
Gnomad4 NFE
AF:
0.198
Gnomad4 OTH
AF:
0.173
Alfa
AF:
0.197
Hom.:
1447
Bravo
AF:
0.178
Asia WGS
AF:
0.174
AC:
605
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
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: rs17798800; hg19: chr13-34950527; API