rs2630488

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 0.506 in 151,956 control chromosomes in the GnomAD database, including 20,067 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 0.51 ( 20067 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.843
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.67729650A>G intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UBA6-DTENST00000500538.7 linkuse as main transcriptn.984-424A>G intron_variant 1
UBA6-DTENST00000656992.1 linkuse as main transcriptn.360-424A>G intron_variant
UBA6-DTENST00000660972.1 linkuse as main transcriptn.272-424A>G intron_variant

Frequencies

GnomAD3 genomes
AF:
0.506
AC:
76847
AN:
151836
Hom.:
20040
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.621
Gnomad AMI
AF:
0.651
Gnomad AMR
AF:
0.468
Gnomad ASJ
AF:
0.520
Gnomad EAS
AF:
0.332
Gnomad SAS
AF:
0.368
Gnomad FIN
AF:
0.484
Gnomad MID
AF:
0.630
Gnomad NFE
AF:
0.469
Gnomad OTH
AF:
0.500
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.506
AC:
76917
AN:
151956
Hom.:
20067
Cov.:
32
AF XY:
0.502
AC XY:
37267
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.621
Gnomad4 AMR
AF:
0.468
Gnomad4 ASJ
AF:
0.520
Gnomad4 EAS
AF:
0.331
Gnomad4 SAS
AF:
0.368
Gnomad4 FIN
AF:
0.484
Gnomad4 NFE
AF:
0.469
Gnomad4 OTH
AF:
0.495
Alfa
AF:
0.480
Hom.:
3066
Bravo
AF:
0.516
Asia WGS
AF:
0.348
AC:
1211
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.68
DANN
Benign
0.58

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: rs2630488; hg19: chr4-68595368; API