rs2630488

Variant summary

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

The ENST00000500538.7(UBA6-DT):​n.984-424A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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

UBA6-DT
ENST00000500538.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.843
Variant links:
Genes affected
UBA6-DT (HGNC:49083): (UBA6 divergent transcript)

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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UBA6-DTENST00000500538.7 linkn.984-424A>G intron_variant Intron 3 of 7 1
UBA6-DTENST00000656992.1 linkn.360-424A>G intron_variant Intron 2 of 4
UBA6-DTENST00000660972.1 linkn.272-424A>G intron_variant Intron 2 of 6

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