rs2351061

Variant summary

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

The NR_169502.1(LINC02751):​n.757-25261T>A 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 0.286 in 151,484 control chromosomes in the GnomAD database, including 6,436 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 0.29 ( 6436 hom., cov: 33)

Consequence

LINC02751
NR_169502.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.522
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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC02751NR_169502.1 linkuse as main transcriptn.757-25261T>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000532242.2 linkuse as main transcriptn.366-25261T>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.286
AC:
43304
AN:
151364
Hom.:
6403
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.288
Gnomad AMI
AF:
0.178
Gnomad AMR
AF:
0.381
Gnomad ASJ
AF:
0.229
Gnomad EAS
AF:
0.422
Gnomad SAS
AF:
0.312
Gnomad FIN
AF:
0.285
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.256
Gnomad OTH
AF:
0.282
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.286
AC:
43389
AN:
151484
Hom.:
6436
Cov.:
33
AF XY:
0.293
AC XY:
21702
AN XY:
74056
show subpopulations
Gnomad4 AFR
AF:
0.289
Gnomad4 AMR
AF:
0.382
Gnomad4 ASJ
AF:
0.229
Gnomad4 EAS
AF:
0.422
Gnomad4 SAS
AF:
0.314
Gnomad4 FIN
AF:
0.285
Gnomad4 NFE
AF:
0.256
Gnomad4 OTH
AF:
0.282
Alfa
AF:
0.270
Hom.:
708
Bravo
AF:
0.290
Asia WGS
AF:
0.352
AC:
1220
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.56
DANN
Benign
0.64

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: rs2351061; hg19: chr11-15700618; API