GeneBe

rs5859158

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.201 in 152,052 control chromosomes in the GnomAD database, including 3,243 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3243 hom., cov: 28)

Consequence


intergenic_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0850
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.69050924delA intergenic_region
LOC105377265XR_001741714.2 linkuse as main transcriptn.3048-788delT intron_variant
LOC105377265XR_938851.2 linkuse as main transcriptn.316-788delT intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.201
AC:
30598
AN:
151934
Hom.:
3242
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.253
Gnomad AMI
AF:
0.272
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.200
Gnomad EAS
AF:
0.175
Gnomad SAS
AF:
0.223
Gnomad FIN
AF:
0.205
Gnomad MID
AF:
0.185
Gnomad NFE
AF:
0.177
Gnomad OTH
AF:
0.197
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.201
AC:
30615
AN:
152052
Hom.:
3243
Cov.:
28
AF XY:
0.201
AC XY:
14931
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.253
Gnomad4 AMR
AF:
0.166
Gnomad4 ASJ
AF:
0.200
Gnomad4 EAS
AF:
0.175
Gnomad4 SAS
AF:
0.224
Gnomad4 FIN
AF:
0.205
Gnomad4 NFE
AF:
0.177
Gnomad4 OTH
AF:
0.197
Alfa
AF:
0.180
Hom.:
328
Bravo
AF:
0.197
Asia WGS
AF:
0.191
AC:
664
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs5859158; hg19: chr4-69916641; API