Genetic Variant UBXN4:c.658-107C>T (chr2-135770464-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014607.4(UBXN4):c.658-107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000336 in 595,220 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

UBXN4
NM_014607.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.16

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN4	NM_014607.4 link	c.658-107C>T		intron_variant	Intron 7 of 12	ENST00000272638.14	NP_055422.1	Q92575

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN4	ENST00000272638.14 link	c.658-107C>T		intron_variant	Intron 7 of 12	1	NM_014607.4	ENSP00000272638.9		Q92575
UBXN4	ENST00000490163.5 link	n.357-107C>T		intron_variant	Intron 3 of 8	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000336

AC:

AN:

595220

Hom.:

AF XY:

0.00000330

AC XY:

AN XY:

302936

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13566

American (AMR)

AF:

0.00

AC:

AN:

11576

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13224

East Asian (EAS)

AF:

0.00

AC:

AN:

27644

South Asian (SAS)

AF:

0.00

AC:

AN:

34724

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40818

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2154

European-Non Finnish (NFE)

AF:

0.00000473

AC:

AN:

422620

Other (OTH)

AF:

0.00

AC:

AN:

28894

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.026

(source)

DANN

Benign

0.69

PhyloP100

-3.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over