dbSNP rs2630488: UBA6-DT:n.984-424A>G (chr4-67729650-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.843

Publications

6 publications found

Variant links:

Genes affected

UBA6-DT (HGNC:49083): (UBA6 divergent transcript)

UBA6-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	TSL
UBA6-DT	ENST00000500538.7 link	n.984-424A>G	intron_variant	Intron 3 of 7	1
UBA6-DT	ENST00000656992.1 link	n.360-424A>G	intron_variant	Intron 2 of 4
UBA6-DT	ENST00000660972.1 link	n.272-424A>G	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

76847

AN:

151836

Hom.:

20040

Cov.:

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.:

AF XY:

0.502

AC XY:

37267

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.621

AC:

25732

AN:

41434

American (AMR)

AF:

0.468

AC:

7143

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.520

AC:

1804

AN:

3470

East Asian (EAS)

AF:

0.331

AC:

1710

AN:

5172

South Asian (SAS)

AF:

0.368

AC:

1774

AN:

4826

European-Finnish (FIN)

AF:

0.484

AC:

5104

AN:

10546

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.469

AC:

31828

AN:

67926

Other (OTH)

AF:

0.495

AC:

1046

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1885

3771

5656

7542

9427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.483

Hom.:

3206

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

(source)

DANN

Benign

0.58

PhyloP100

-0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over