rs4881131

Variant summary

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

The ENST00000669318.1(LINC02668):​n.1852+2979C>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 0.236 in 152,056 control chromosomes in the GnomAD database, including 4,405 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 0.24 ( 4405 hom., cov: 32)

Consequence

LINC02668
ENST00000669318.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.657
Variant links:
Genes affected
LINC02668 (HGNC:54154): (long intergenic non-protein coding RNA 2668)

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=-0.91).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LINC02668XR_001747318.3 linkuse as main transcriptn.1852+2979C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02668ENST00000669318.1 linkuse as main transcriptn.1852+2979C>T intron_variant, non_coding_transcript_variant
LINC02668ENST00000417149.2 linkuse as main transcriptn.887+2979C>T intron_variant, non_coding_transcript_variant 3
LINC02668ENST00000655354.1 linkuse as main transcriptn.539+2979C>T intron_variant, non_coding_transcript_variant
LINC02668ENST00000665182.1 linkuse as main transcriptn.539+2979C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.236
AC:
35807
AN:
151938
Hom.:
4393
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.165
Gnomad AMI
AF:
0.283
Gnomad AMR
AF:
0.283
Gnomad ASJ
AF:
0.199
Gnomad EAS
AF:
0.242
Gnomad SAS
AF:
0.303
Gnomad FIN
AF:
0.321
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.251
Gnomad OTH
AF:
0.234
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.236
AC:
35857
AN:
152056
Hom.:
4405
Cov.:
32
AF XY:
0.242
AC XY:
17960
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.165
Gnomad4 AMR
AF:
0.284
Gnomad4 ASJ
AF:
0.199
Gnomad4 EAS
AF:
0.243
Gnomad4 SAS
AF:
0.303
Gnomad4 FIN
AF:
0.321
Gnomad4 NFE
AF:
0.251
Gnomad4 OTH
AF:
0.235
Alfa
AF:
0.238
Hom.:
5889
Bravo
AF:
0.228
Asia WGS
AF:
0.311
AC:
1082
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.9
DANN
Benign
0.53

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: rs4881131; hg19: chr10-3295673; API