Genetic Variant UBBP4:n.1250T>C (chr17-22204923-T-C) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The ENST00000584755.3(UBBP4):n.1250T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00081 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000043 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

UBBP4
ENST00000584755.3 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.67

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: Likely_benign. The variant received -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 17-22204923-T-C is Benign according to our data. Variant chr17-22204923-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 3234342.Status of the report is criteria_provided_single_submitter, 1 stars.

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.1228T>C		non_coding_transcript_exon	Exon 2 of 2
	UBBP4	NR_176224.1		n.1186T>C		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
UBBP4	ENST00000584755.3	TSL:1	n.1250T>C	non_coding_transcript_exon	Exon 2 of 2
UBBP4	ENST00000583708.6	TSL:6	n.831T>C	non_coding_transcript_exon	Exon 1 of 1
UBBP4	ENST00000648259.1		n.1193T>C	non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.000818

AC:

111

AN:

135674

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000997

Gnomad AMI

AF:

0.00256

Gnomad AMR

AF:

0.000216

Gnomad ASJ

AF:

0.000627

Gnomad EAS

AF:

0.00323

Gnomad SAS

AF:

0.00148

Gnomad FIN

AF:

0.000534

Gnomad MID

AF:

0.0183

Gnomad NFE

AF:

0.000598

Gnomad OTH

AF:

0.00107

GnomAD2 exomes

AF:

0.0000450

AC:

AN:

244194

AF XY:

0.0000681

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000305

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000269

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000431

AC:

AN:

1436924

Hom.:

Cov.:

AF XY:

0.0000532

AC XY:

AN XY:

714740

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

32410

American (AMR)

AF:

0.0000975

AC:

AN:

41026

Ashkenazi Jewish (ASJ)

AF:

0.0000393

AC:

AN:

25428

East Asian (EAS)

AF:

0.0000791

AC:

AN:

37924

South Asian (SAS)

AF:

0.000191

AC:

AN:

83620

European-Finnish (FIN)

AF:

0.0000189

AC:

AN:

52890

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5318

European-Non Finnish (NFE)

AF:

0.0000273

AC:

AN:

1099230

Other (OTH)

AF:

0.000118

AC:

AN:

59078

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.360

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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000810

AC:

110

AN:

135776

Hom.:

Cov.:

AF XY:

0.000644

AC XY:

AN XY:

66742

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000995

AC:

AN:

36198

American (AMR)

AF:

0.000215

AC:

AN:

13932

Ashkenazi Jewish (ASJ)

AF:

0.000627

AC:

AN:

3188

East Asian (EAS)

AF:

0.00324

AC:

AN:

4324

South Asian (SAS)

AF:

0.00148

AC:

AN:

4058

European-Finnish (FIN)

AF:

0.000534

AC:

AN:

9370

Middle Eastern (MID)

AF:

0.0147

AC:

AN:

204

European-Non Finnish (NFE)

AF:

0.000598

AC:

AN:

61826

Other (OTH)

AF:

0.00106

AC:

AN:

1894

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.242

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:

0.00723

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.36

PhyloP100

1.7

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

2.1

Mutation Taster

=98/2

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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