rs759563

Variant summary

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

The ENST00000581801.7(LINC00511):​n.658-51427G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,972 control chromosomes in the GnomAD database, including 24,617 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 0.55 ( 24617 hom., cov: 32)

Consequence

LINC00511
ENST00000581801.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.870
Variant links:
Genes affected
LINC00511 (HGNC:43564): (long intergenic non-protein coding RNA 511)

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 (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC00511ENST00000581801.7 linkn.658-51427G>A intron_variant Intron 2 of 2 3
LINC00511ENST00000648088.1 linkn.491-51427G>A intron_variant Intron 1 of 1
LINC00511ENST00000648248.1 linkn.394+53489G>A intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.554
AC:
84169
AN:
151854
Hom.:
24577
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.736
Gnomad AMI
AF:
0.658
Gnomad AMR
AF:
0.602
Gnomad ASJ
AF:
0.575
Gnomad EAS
AF:
0.302
Gnomad SAS
AF:
0.446
Gnomad FIN
AF:
0.408
Gnomad MID
AF:
0.602
Gnomad NFE
AF:
0.480
Gnomad OTH
AF:
0.570
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.554
AC:
84267
AN:
151972
Hom.:
24617
Cov.:
32
AF XY:
0.550
AC XY:
40885
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.736
Gnomad4 AMR
AF:
0.602
Gnomad4 ASJ
AF:
0.575
Gnomad4 EAS
AF:
0.302
Gnomad4 SAS
AF:
0.444
Gnomad4 FIN
AF:
0.408
Gnomad4 NFE
AF:
0.480
Gnomad4 OTH
AF:
0.568
Alfa
AF:
0.502
Hom.:
10803
Bravo
AF:
0.577
Asia WGS
AF:
0.412
AC:
1432
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
0.13
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: rs759563; hg19: chr17-70370888; API