rs371199833

Variant names:

• chr20-3110146-C-A
• rs371199833
• NM_014948.4:c.1586G>T

Your query was ambiguous. Multiple possible variants found:

• chr20-3110146-C-A
• chr20-3110146-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_014948.4(UBOX5):​c.1586G>T​(p.Arg529Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict 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: 33)
• Consequence: UBOX5 NM_014948.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

UBOX5 (HGNC:17777): (U-box domain containing 5) This gene encodes a U-box domain containing protein. The encoded protein interacts with E2 enzymes and may play a role in the ubiquitination pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

UBOX5-AS1 (HGNC:44111): (UBOX5 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09990826).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBOX5	NM_014948.4	c.1586G>T	p.Arg529Leu	missense_variant	Exon 5 of 5	ENST00000217173.7	NP_055763.1
UBOX5	NM_199415.3	c.1424G>T	p.Arg475Leu	missense_variant	Exon 4 of 4		NP_955447.1
UBOX5	NM_001267584.2	c.*42G>T		3_prime_UTR_variant	Exon 5 of 5		NP_001254513.1
UBOX5-AS1	NR_038395.1	n.938-132C>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBOX5	ENST00000217173.7	c.1586G>T	p.Arg529Leu	missense_variant	Exon 5 of 5	1	NM_014948.4	ENSP00000217173.2
UBOX5	ENST00000348031.6	c.1424G>T	p.Arg475Leu	missense_variant	Exon 4 of 4	1		ENSP00000311726.3
UBOX5-AS1	ENST00000446537.5	n.936-132C>A		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.080
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	5.7
DANN	Benign	0.97
DEOGEN2	Benign	0.030	T;.
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.76	T;T
M_CAP	Benign	0.043	D
MetaRNN	Benign	0.10	T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	1.7	L;.
PrimateAI	Benign	0.21	T
PROVEAN	Benign	-1.1	N;N
REVEL	Benign	0.089
Sift	Uncertain	0.019	D;T
Sift4G	Uncertain	0.054	T;T
Polyphen		0.42	B;.
Vest4		0.26
MutPred		0.38		Loss of disorder (P = 0.0384);.;
MVP		0.60
MPC		0.42
ClinPred		0.24	T
GERP RS		-5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.052
gMVP		0.32

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

LitVar

Other links and lift over

dbSNP: rs371199833; hg19: chr20-3090792;