GeneBe

rs2159942

Positions:

Variant summary

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

The variant allele was found at a frequency of 0.216 in 152,180 control chromosomes in the GnomAD database, including 3,813 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 0.22 ( 3813 hom., cov: 31)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.297
Variant links:
Genes affected

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 (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.14062350A>C intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZNF519ENST00000592345.5 linkuse as main transcriptn.714-4835T>G intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.216
AC:
32828
AN:
152062
Hom.:
3816
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.194
Gnomad AMI
AF:
0.277
Gnomad AMR
AF:
0.181
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.321
Gnomad MID
AF:
0.244
Gnomad NFE
AF:
0.243
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.216
AC:
32823
AN:
152180
Hom.:
3813
Cov.:
31
AF XY:
0.214
AC XY:
15933
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.194
Gnomad4 AMR
AF:
0.181
Gnomad4 ASJ
AF:
0.220
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.106
Gnomad4 FIN
AF:
0.321
Gnomad4 NFE
AF:
0.243
Gnomad4 OTH
AF:
0.218
Alfa
AF:
0.207
Hom.:
1685
Bravo
AF:
0.204
Asia WGS
AF:
0.0720
AC:
252
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
1.7
DANN
Benign
0.69

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: rs2159942; hg19: chr18-14062349; API