Genetic Variant UBBP4:n.1034G>A (chr17-22204707-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000584755.3(UBBP4):n.1034G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0000486 in 1,585,510 control chromosomes in the GnomAD database, including 1 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 0.000056 ( 1 hom., cov: 29)

Exomes 𝑓: 0.000048 ( 0 hom. )

Consequence

UBBP4
ENST00000584755.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.89

Publications

0 publications found

Variant links:

Genes affected

UBBP4 (HGNC:):

UBBP4 links:

UBBP4 (HGNC:12467): (ubiquitin B pseudogene 4)

UBBP4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584755.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBBP4	NR_144546.2		n.1012G>A		non_coding_transcript_exon	Exon 2 of 2
	UBBP4	NR_176224.1		n.970G>A		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
UBBP4	ENST00000584755.3	TSL:1	n.1034G>A	non_coding_transcript_exon	Exon 2 of 2
UBBP4	ENST00000583708.6	TSL:6	n.615G>A	non_coding_transcript_exon	Exon 1 of 1
UBBP4	ENST00000648259.1		n.977G>A	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0000560

AC:

AN:

125098

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000927

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000338

Gnomad OTH

AF:

0.00115

GnomAD2 exomes

AF:

0.0000361

AC:

AN:

249252

AF XY:

0.0000371

show subpopulations

Gnomad AFR exome

AF:

0.0000618

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.0000996

Gnomad EAS exome

AF:

0.0000550

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.0000442

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000479

AC:

AN:

1460412

Hom.:

Cov.:

AF XY:

0.0000496

AC XY:

AN XY:

726402

show subpopulations

African (AFR)

AF:

0.0000598

AC:

AN:

33430

American (AMR)

AF:

0.0000449

AC:

AN:

44518

Ashkenazi Jewish (ASJ)

AF:

0.0000766

AC:

AN:

26102

East Asian (EAS)

AF:

0.000101

AC:

AN:

39660

South Asian (SAS)

AF:

0.0000349

AC:

AN:

85918

European-Finnish (FIN)

AF:

0.0000187

AC:

AN:

53410

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5744

European-Non Finnish (NFE)

AF:

0.0000477

AC:

AN:

1111324

Other (OTH)

AF:

0.0000497

AC:

AN:

60306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000560

AC:

AN:

125098

Hom.:

Cov.:

AF XY:

0.0000662

AC XY:

AN XY:

60408

show subpopulations

African (AFR)

AF:

0.0000927

AC:

AN:

32358

American (AMR)

AF:

0.00

AC:

AN:

12414

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3098

East Asian (EAS)

AF:

0.00

AC:

AN:

4086

South Asian (SAS)

AF:

0.00

AC:

AN:

3844

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7510

Middle Eastern (MID)

AF:

0.00

AC:

AN:

178

European-Non Finnish (NFE)

AF:

0.0000338

AC:

AN:

59242

Other (OTH)

AF:

0.00115

AC:

AN:

1738

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.0000396

Hom.:

Bravo

AF:

0.0000680

EpiCase

AF:

0.0000545

EpiControl

AF:

0.0000594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

(source)

DANN

Benign

0.47

PhyloP100

3.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over