rs10188066

Variant names:

• chr2-135781943-G-A
• rs10188066
• NM_014607.4:c.1389-806G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-135781943-G-A
• chr2-135781943-G-C

Variant summary

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

The NM_014607.4(UBXN4):​c.1389-806G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,032 control chromosomes in the GnomAD database, including 30,366 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 0.61 (30366 hom., cov: 31)
• Consequence: UBXN4 NM_014607.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 12 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBXN4	NM_014607.4	c.1389-806G>A		intron_variant	Intron 12 of 12	ENST00000272638.14	NP_055422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBXN4	ENST00000272638.14	c.1389-806G>A		intron_variant	Intron 12 of 12	1	NM_014607.4	ENSP00000272638.9
UBXN4	ENST00000490163.5	n.1088-806G>A		intron_variant	Intron 8 of 8	2

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92186 AN: 151914 Hom.: 30365 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.607 AC: 92217 AN: 152032 Hom.: 30366 Cov.: 31 AF XY: 0.598 AC XY: 44451 AN XY: 74316

African (AFR) AF: 0.385 AC: 15970 AN: 41462

American (AMR) AF: 0.507 AC: 7754 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1490 AN: 3462

East Asian (EAS) AF: 0.628 AC: 3237 AN: 5152

South Asian (SAS) AF: 0.456 AC: 2193 AN: 4812

European-Finnish (FIN) AF: 0.747 AC: 7902 AN: 10572

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.761 AC: 51714 AN: 67970

Other (OTH) AF: 0.542 AC: 1144 AN: 2112

Alfa AF: 0.667 Hom.: 83606

Bravo AF: 0.584

Asia WGS AF: 0.514 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.29
PhyloP100		-0.51
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: rs10188066; hg19: chr2-136539513;