rs2226121

Variant summary

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

The NR_149135.1(LINC02542):​n.206+5724C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,178 control chromosomes in the GnomAD database, including 897 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 0.10 ( 897 hom., cov: 32)

Consequence

LINC02542
NR_149135.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330
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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02542NR_149135.1 linkuse as main transcriptn.206+5724C>T intron_variant
LOC107986617XR_001744231.2 linkuse as main transcriptn.751-17621G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02542ENST00000660637.1 linkuse as main transcriptn.156+5809C>T intron_variant
LINC02542ENST00000663543.1 linkuse as main transcriptn.290-37831C>T intron_variant
LINC02542ENST00000666226.1 linkuse as main transcriptn.121+5809C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.105
AC:
15913
AN:
152060
Hom.:
895
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0813
Gnomad AMI
AF:
0.127
Gnomad AMR
AF:
0.157
Gnomad ASJ
AF:
0.0877
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.155
Gnomad FIN
AF:
0.0818
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.108
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.105
AC:
15944
AN:
152178
Hom.:
897
Cov.:
32
AF XY:
0.106
AC XY:
7878
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.0816
Gnomad4 AMR
AF:
0.157
Gnomad4 ASJ
AF:
0.0877
Gnomad4 EAS
AF:
0.116
Gnomad4 SAS
AF:
0.156
Gnomad4 FIN
AF:
0.0818
Gnomad4 NFE
AF:
0.107
Gnomad4 OTH
AF:
0.108
Alfa
AF:
0.109
Hom.:
695
Bravo
AF:
0.109
Asia WGS
AF:
0.149
AC:
519
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
1.7
DANN
Benign
0.28

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: rs2226121; hg19: chr6-82805553; API