rs167685

Variant summary

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

The ENST00000636877.1(LINC02550):​n.838-5615A>G 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 0.374 in 151,922 control chromosomes in the GnomAD database, including 10,954 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 0.37 ( 10954 hom., cov: 32)

Consequence

LINC02550
ENST00000636877.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.137
Variant links:
Genes affected
LINC02550 (HGNC:53585): (long intergenic non-protein coding RNA 2550)

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=-0.98).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC102723966XR_428993.4 linkuse as main transcriptn.208-309T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LINC02550ENST00000636877.1 linkuse as main transcriptn.838-5615A>G intron_variant, non_coding_transcript_variant 5
ENST00000659487.1 linkuse as main transcriptn.208-309T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.374
AC:
56806
AN:
151804
Hom.:
10921
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.434
Gnomad AMI
AF:
0.281
Gnomad AMR
AF:
0.466
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.355
Gnomad SAS
AF:
0.316
Gnomad FIN
AF:
0.274
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.344
Gnomad OTH
AF:
0.374
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.374
AC:
56874
AN:
151922
Hom.:
10954
Cov.:
32
AF XY:
0.375
AC XY:
27829
AN XY:
74252
show subpopulations
Gnomad4 AFR
AF:
0.435
Gnomad4 AMR
AF:
0.466
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.355
Gnomad4 SAS
AF:
0.314
Gnomad4 FIN
AF:
0.274
Gnomad4 NFE
AF:
0.344
Gnomad4 OTH
AF:
0.369
Alfa
AF:
0.350
Hom.:
1196
Bravo
AF:
0.394
Asia WGS
AF:
0.356
AC:
1236
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.6
DANN
Benign
0.77

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: rs167685; hg19: chr11-110968650; API