rs6889886

Positions:

Variant summary

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

The ENST00000653645.1(LINC01511):​n.437-3172G>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 0.235 in 152,158 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 0.23 ( 4405 hom., cov: 33)

Consequence

LINC01511
ENST00000653645.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.272
Variant links:
Genes affected
LINC01511 (HGNC:51200): (long intergenic non-protein coding RNA 1511)

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 (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC01511ENST00000653645.1 linkuse as main transcriptn.437-3172G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.235
AC:
35707
AN:
152040
Hom.:
4399
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.203
Gnomad AMI
AF:
0.275
Gnomad AMR
AF:
0.211
Gnomad ASJ
AF:
0.317
Gnomad EAS
AF:
0.0541
Gnomad SAS
AF:
0.0985
Gnomad FIN
AF:
0.288
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.269
Gnomad OTH
AF:
0.260
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.235
AC:
35709
AN:
152158
Hom.:
4405
Cov.:
33
AF XY:
0.231
AC XY:
17204
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.203
Gnomad4 AMR
AF:
0.211
Gnomad4 ASJ
AF:
0.317
Gnomad4 EAS
AF:
0.0539
Gnomad4 SAS
AF:
0.0983
Gnomad4 FIN
AF:
0.288
Gnomad4 NFE
AF:
0.269
Gnomad4 OTH
AF:
0.257
Alfa
AF:
0.249
Hom.:
719
Bravo
AF:
0.230
Asia WGS
AF:
0.0970
AC:
337
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
2.3
DANN
Benign
0.30

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: rs6889886; hg19: chr5-1358822; API