Genetic Variant GUSBP5:n.179-26013A>G (chr4-143782301-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 ENST00000499587.2(GUSBP5):n.179-26013A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,120 control chromosomes in the GnomAD database, including 5,961 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 0.26 ( 5961 hom., cov: 32)

Consequence

GUSBP5
ENST00000499587.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143

Publications

4 publications found

Variant links:

Genes affected

GUSBP5 (HGNC:):

GUSBP5 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 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
GUSBP5	ENST00000499587.2 link	n.179-26013A>G	intron_variant	Intron 2 of 6	4
GUSBP5	ENST00000641328.2 link	n.1005+43184A>G	intron_variant	Intron 3 of 6
GUSBP5	ENST00000641556.1 link	n.250+43184A>G	intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40237

AN:

152002

Hom.:

5957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.149

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.0472

Gnomad SAS

AF:

0.327

Gnomad FIN

AF:

0.325

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.290

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.265

AC:

40257

AN:

152120

Hom.:

5961

Cov.:

AF XY:

0.266

AC XY:

19794

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.149

AC:

6190

AN:

41520

American (AMR)

AF:

0.325

AC:

4969

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1208

AN:

3470

East Asian (EAS)

AF:

0.0471

AC:

244

AN:

5184

South Asian (SAS)

AF:

0.327

AC:

1578

AN:

4826

European-Finnish (FIN)

AF:

0.325

AC:

3436

AN:

10582

Middle Eastern (MID)

AF:

0.354

AC:

104

AN:

294

European-Non Finnish (NFE)

AF:

0.320

AC:

21768

AN:

67956

Other (OTH)

AF:

0.285

AC:

603

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1453

2906

4358

5811

7264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.287

Hom.:

857

Bravo

AF:

0.257

Asia WGS

AF:

0.205

AC:

717

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

0.14

Splicing

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

Publications

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chr4-143782301-A-G

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