rs1372502364

Variant names:

• chr20-3115331-G-A
• rs1372502364
• NM_014948.4:c.1391C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-3115331-G-A
• chr20-3115331-G-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.1391C>T​(p.Thr464Ile) 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. 14/21 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: 32)
• Consequence: UBOX5 NM_014948.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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=0.119062096).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBOX5	NM_014948.4	c.1391C>T	p.Thr464Ile	missense_variant	Exon 4 of 5	ENST00000217173.7	NP_055763.1
UBOX5	NM_001267584.2	c.1391C>T	p.Thr464Ile	missense_variant	Exon 4 of 5		NP_001254513.1
UBOX5	NM_199415.3	c.1256-5017C>T		intron_variant	Intron 3 of 3		NP_955447.1
UBOX5-AS1	NR_038395.1	n.1308+3579G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBOX5	ENST00000217173.7	c.1391C>T	p.Thr464Ile	missense_variant	Exon 4 of 5	1	NM_014948.4	ENSP00000217173.2
UBOX5	ENST00000348031.6	c.1256-5017C>T		intron_variant	Intron 3 of 3	1		ENSP00000311726.3
UBOX5-AS1	ENST00000446537.5	n.1306+3579G>A		intron_variant	Intron 5 of 6	2
UBOX5-AS1	ENST00000454019.1	n.191-1158G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.086
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.058	T
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.17
FATHMM_MKL	Benign	0.57	D
LIST_S2	Benign	0.60	T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.9	L
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.094
Sift	Uncertain	0.015	D
Sift4G	Uncertain	0.032	D
Polyphen		0.26	B
Vest4		0.18
MutPred		0.25		Loss of helix (P = 0.028);
MVP		0.52
MPC		0.29
ClinPred		0.53	D
GERP RS		4.0
Varity_R		0.17
gMVP		0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs1372502364; hg19: chr20-3095977;