rs9287442

Variant names:

• chr2-135765140-A-G
• rs9287442
• NM_014607.4:c.602+3229A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-135765140-A-G
• chr2-135765140-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014607.4(UBXN4):​c.602+3229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,066 control chromosomes in the GnomAD database, including 29,515 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 0.60 (29515 hom., cov: 33)
• Consequence: UBXN4 NM_014607.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534
• Publications: 16 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN4	NM_014607.4	c.602+3229A>G		intron_variant	Intron 6 of 12	ENST00000272638.14	NP_055422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN4	ENST00000272638.14	c.602+3229A>G		intron_variant	Intron 6 of 12	1	NM_014607.4	ENSP00000272638.9
UBXN4	ENST00000490163.5	n.302-4629A>G		intron_variant	Intron 2 of 8	2

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90515 AN: 151948 Hom.: 29512 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.535

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.595 AC: 90546 AN: 152066 Hom.: 29515 Cov.: 33 AF XY: 0.585 AC XY: 43504 AN XY: 74318

African (AFR) AF: 0.383 AC: 15882 AN: 41464

American (AMR) AF: 0.478 AC: 7309 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3466

East Asian (EAS) AF: 0.441 AC: 2283 AN: 5182

South Asian (SAS) AF: 0.444 AC: 2140 AN: 4816

European-Finnish (FIN) AF: 0.748 AC: 7892 AN: 10556

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51648 AN: 67980

Other (OTH) AF: 0.531 AC: 1122 AN: 2112

Alfa AF: 0.682 Hom.: 58419

Bravo AF: 0.569

Asia WGS AF: 0.441 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9287442; hg19: chr2-136522710;