dbSNP rs2304601: UBXN4:c.658-107C>A (chr2-135770464-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_014607.4(UBXN4):c.658-107C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 746,180 control chromosomes in the GnomAD database, including 11,743 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 0.17 ( 2538 hom., cov: 32)

Exomes 𝑓: 0.16 ( 9205 hom. )

Consequence

UBXN4
NM_014607.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.16

Publications

3 publications found

Variant links:

Genes affected

UBXN4 (HGNC:14860): (UBX domain protein 4) UBXD2 is an integral membrane protein of the endoplasmic reticulum (ER) that binds valosin-containing protein (VCP; MIM 601023) and promotes ER-associated protein degradation (ERAD) (Liang et al., 2006 [PubMed 16968747]).[supplied by OMIM, Mar 2008]

UBXN4 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_014607.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014607.4. 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
	UBXN4	NM_014607.4	MANE Select	c.658-107C>A		intron	N/A	NP_055422.1	Q92575

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBXN4	ENST00000272638.14	TSL:1 MANE Select	c.658-107C>A	intron	N/A	ENSP00000272638.9	Q92575
UBXN4	ENST00000928826.1		c.745-107C>A	intron	N/A	ENSP00000598885.1
UBXN4	ENST00000928825.1		c.688-107C>A	intron	N/A	ENSP00000598884.1

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25975

AN:

152076

Hom.:

2539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.442

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.160

Gnomad OTH

AF:

0.239

GnomAD4 exome

AF:

0.160

AC:

94759

AN:

593986

Hom.:

9205

AF XY:

0.164

AC XY:

49485

AN XY:

302268

show subpopulations

African (AFR)

AF:

0.154

AC:

2078

AN:

13536

American (AMR)

AF:

0.207

AC:

2391

AN:

11540

Ashkenazi Jewish (ASJ)

AF:

0.437

AC:

5761

AN:

13180

East Asian (EAS)

AF:

0.145

AC:

4009

AN:

27612

South Asian (SAS)

AF:

0.219

AC:

7588

AN:

34598

European-Finnish (FIN)

AF:

0.133

AC:

5434

AN:

40770

Middle Eastern (MID)

AF:

0.411

AC:

882

AN:

2144

European-Non Finnish (NFE)

AF:

0.145

AC:

61030

AN:

421774

Other (OTH)

AF:

0.194

AC:

5586

AN:

28832

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3633

7266

10900

14533

18166

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1380

2760

4140

5520

6900

<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:

0.171

AC:

25989

AN:

152194

Hom.:

2538

Cov.:

AF XY:

0.173

AC XY:

12883

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.143

AC:

5924

AN:

41540

American (AMR)

AF:

0.230

AC:

3519

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.442

AC:

1536

AN:

3472

East Asian (EAS)

AF:

0.180

AC:

934

AN:

5178

South Asian (SAS)

AF:

0.219

AC:

1056

AN:

4818

European-Finnish (FIN)

AF:

0.131

AC:

1381

AN:

10572

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.160

AC:

10871

AN:

68014

Other (OTH)

AF:

0.242

AC:

513

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1063

2126

3190

4253

5316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.169

Hom.:

328

Bravo

AF:

0.175

Asia WGS

AF:

0.182

AC:

634

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.020

(source)

DANN

Benign

0.60

PhyloP100

-3.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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