20-3138909-T-G

Position:

• chr20-3138909-T-G

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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/exons	MANE	UniProt
UBOX5	NM_014948.4	c.-41-15503A>C		intron_variant		ENST00000217173.7
UBOX5-AS1	NR_038395.1	n.1464+2751T>G		intron_variant, non_coding_transcript_variant
UBOX5	NM_001267584.2	c.-41-15503A>C		intron_variant
UBOX5	NM_199415.3	c.-41-15503A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBOX5	ENST00000217173.7	c.-41-15503A>C		intron_variant		1	NM_014948.4	P1
UBOX5	ENST00000348031.6	c.-41-15503A>C		intron_variant		1
UBOX5-AS1	ENST00000446537.5	n.1462+2751T>G		intron_variant, non_coding_transcript_variant		2
UBOX5	ENST00000449731.1	c.-41-15503A>C		intron_variant		5

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

Gnomad4 AFR AF: 0.0718

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.0967

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.250

Alfa AF: 0.333 Hom.: 12159

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

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: rs857252; hg19: chr20-3119555;