Genetic Variant UBXN7:c.468+63T>A (chr3-196391750-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015562.2(UBXN7):c.468+63T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 1,215,114 control chromosomes in the GnomAD database, including 86,339 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 0.38 ( 11433 hom., cov: 29)

Exomes 𝑓: 0.36 ( 74906 hom. )

Consequence

UBXN7
NM_015562.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13

Publications

0 publications found

Variant links:

Genes affected

UBXN7 (HGNC:29119): (UBX domain protein 7) Enables ubiquitin binding activity and ubiquitin protein ligase binding activity. Located in nuclear body. Part of VCP-NPL4-UFD1 AAA ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]

UBXN7 links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015562.2. 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
	UBXN7	NM_015562.2	MANE Select	c.468+63T>A		intron	N/A	NP_056377.1	O94888

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBXN7	ENST00000296328.9	TSL:1 MANE Select	c.468+63T>A	intron	N/A	ENSP00000296328.4	O94888
UBXN7	ENST00000428095.1	TSL:1	c.-18-19708T>A	intron	N/A	ENSP00000397256.1	C9JAT7
UBXN7	ENST00000897727.1		c.468+63T>A	intron	N/A	ENSP00000567786.1

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57074

AN:

151494

Hom.:

11415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.347

Gnomad AMI

AF:

0.271

Gnomad AMR

AF:

0.468

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.824

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.314

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.377

GnomAD4 exome

AF:

0.360

AC:

382720

AN:

1063504

Hom.:

74906

AF XY:

0.357

AC XY:

194026

AN XY:

543106

show subpopulations

African (AFR)

AF:

0.329

AC:

7888

AN:

23944

American (AMR)

AF:

0.491

AC:

15336

AN:

31230

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

6841

AN:

20674

East Asian (EAS)

AF:

0.843

AC:

30648

AN:

36372

South Asian (SAS)

AF:

0.291

AC:

20725

AN:

71194

European-Finnish (FIN)

AF:

0.296

AC:

14681

AN:

49634

Middle Eastern (MID)

AF:

0.309

AC:

1484

AN:

4806

European-Non Finnish (NFE)

AF:

0.345

AC:

268631

AN:

779400

Other (OTH)

AF:

0.356

AC:

16486

AN:

46250

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

10505

21009

31514

42018

52523

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7640

15280

22920

30560

38200

<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:

0.377

AC:

57124

AN:

151610

Hom.:

11433

Cov.:

AF XY:

0.376

AC XY:

27849

AN XY:

74086

show subpopulations

African (AFR)

AF:

0.347

AC:

14339

AN:

41328

American (AMR)

AF:

0.467

AC:

7091

AN:

15172

Ashkenazi Jewish (ASJ)

AF:

0.338

AC:

1171

AN:

3468

East Asian (EAS)

AF:

0.825

AC:

4252

AN:

5152

South Asian (SAS)

AF:

0.313

AC:

1503

AN:

4806

European-Finnish (FIN)

AF:

0.292

AC:

3072

AN:

10514

Middle Eastern (MID)

AF:

0.310

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.362

AC:

24558

AN:

67870

Other (OTH)

AF:

0.382

AC:

802

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

1578

3156

4735

6313

7891

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

548

1096

1644

2192

2740

<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:

0.363

Hom.:

1291

Bravo

AF:

0.395

Asia WGS

AF:

0.529

AC:

1838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.32

(source)

DANN

Benign

0.17

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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