20-3138909-T-G

Variant names:

• chr20-3138909-T-G
• rs857252
• NM_014948.4:c.-41-15503A>C

Variant summary

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

The NM_014948.4(UBOX5):​c.-41-15503A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,906 control chromosomes in the GnomAD database, including 6,722 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 0.26 (6722 hom., cov: 31)
• Consequence: UBOX5 NM_014948.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBOX5	NM_014948.4	c.-41-15503A>C		intron_variant	Intron 1 of 4	ENST00000217173.7	NP_055763.1
UBOX5	NM_001267584.2	c.-41-15503A>C		intron_variant	Intron 1 of 4		NP_001254513.1
UBOX5	NM_199415.3	c.-41-15503A>C		intron_variant	Intron 1 of 3		NP_955447.1
UBOX5-AS1	NR_038395.1	n.1464+2751T>G		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBOX5	ENST00000217173.7	c.-41-15503A>C		intron_variant	Intron 1 of 4	1	NM_014948.4	ENSP00000217173.2
UBOX5	ENST00000348031.6	c.-41-15503A>C		intron_variant	Intron 1 of 3	1		ENSP00000311726.3
UBOX5	ENST00000449731.1	c.-41-15503A>C		intron_variant	Intron 2 of 3	5		ENSP00000404364.1
UBOX5-AS1	ENST00000446537.5	n.1462+2751T>G		intron_variant	Intron 6 of 6	2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40173 AN: 151788 Hom.: 6720 Cov.: 31

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.264 AC: 40175 AN: 151906 Hom.: 6722 Cov.: 31 AF XY: 0.266 AC XY: 19731 AN XY: 74224

African (AFR) AF: 0.0718 AC: 2975 AN: 41422

American (AMR) AF: 0.258 AC: 3939 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3470

East Asian (EAS) AF: 0.0967 AC: 500 AN: 5168

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4814

European-Finnish (FIN) AF: 0.426 AC: 4481 AN: 10528

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24999 AN: 67952

Other (OTH) AF: 0.250 AC: 528 AN: 2110

Alfa AF: 0.322 Hom.: 15755

Bravo AF: 0.246

Asia WGS AF: 0.163 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-1.1
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: rs857252; hg19: chr20-3119555;