rs61457372

Variant summary

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

The ENST00000581801.7(LINC00511):​n.658-40313A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,476 control chromosomes in the GnomAD database, including 29,221 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 0.62 ( 29221 hom., cov: 29)

Consequence

LINC00511
ENST00000581801.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228
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=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 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.658-40313A>G intron_variant Intron 2 of 2 3
LINC00511ENST00000648088.1 linkn.491-40313A>G intron_variant Intron 1 of 1
LINC00511ENST00000648248.1 linkn.394+64603A>G intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.615
AC:
93123
AN:
151356
Hom.:
29215
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.515
Gnomad AMI
AF:
0.692
Gnomad AMR
AF:
0.473
Gnomad ASJ
AF:
0.621
Gnomad EAS
AF:
0.728
Gnomad SAS
AF:
0.695
Gnomad FIN
AF:
0.688
Gnomad MID
AF:
0.659
Gnomad NFE
AF:
0.681
Gnomad OTH
AF:
0.616
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.615
AC:
93163
AN:
151476
Hom.:
29221
Cov.:
29
AF XY:
0.614
AC XY:
45411
AN XY:
73990
show subpopulations
Gnomad4 AFR
AF:
0.515
Gnomad4 AMR
AF:
0.472
Gnomad4 ASJ
AF:
0.621
Gnomad4 EAS
AF:
0.728
Gnomad4 SAS
AF:
0.695
Gnomad4 FIN
AF:
0.688
Gnomad4 NFE
AF:
0.681
Gnomad4 OTH
AF:
0.619
Alfa
AF:
0.648
Hom.:
4963
Bravo
AF:
0.594
Asia WGS
AF:
0.704
AC:
2451
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
5.4
DANN
Benign
0.73

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: rs61457372; hg19: chr17-70359774; API