Genetic Variant NM_015562.2: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:

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=-0.85).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN7	NM_015562.2 link	c.468+63T>A		intron_variant	Intron 5 of 10	ENST00000296328.9	NP_056377.1	O94888
UBXN7	XM_011512671.3 link	c.24+63T>A		intron_variant	Intron 4 of 9		XP_011510973.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
UBXN7	ENST00000296328.9 link	c.468+63T>A	intron_variant	Intron 5 of 10	1	NM_015562.2	ENSP00000296328.4	O94888
UBXN7	ENST00000428095.1 link	c.-18-19708T>A	intron_variant	Intron 1 of 6	1		ENSP00000397256.1	C9JAT7
UBXN7	ENST00000381887.8 link	c.402+63T>A	intron_variant	Intron 4 of 9	3		ENSP00000371311.4	H7BYF4
UBXN7	ENST00000429160.1 link	n.*92+63T>A	intron_variant	Intron 4 of 9	2		ENSP00000397238.1	F8WB69

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over