NM_014517.5:c.114-5704A>G

Variant names:

• chr3-33431445-T-C
• rs1807844
• NM_014517.5:c.114-5704A>G

Variant summary

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

The NM_014517.5(UBP1):​c.114-5704A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,930 control chromosomes in the GnomAD database, including 5,952 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 (5952 hom., cov: 32)
• Consequence: UBP1 NM_014517.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 4 publications found

Genes affected

UBP1 (HGNC:12507): (upstream binding protein 1) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of viral transcription and positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014517.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBP1	NM_014517.5	MANE Select	c.114-5704A>G		intron	N/A	NP_055332.3
	UBP1	NM_001128161.2		c.114-5704A>G		intron	N/A	NP_001121633.1
	UBP1	NM_001128160.2		c.114-5704A>G		intron	N/A	NP_001121632.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBP1	ENST00000283629.8	TSL:1 MANE Select	c.114-5704A>G		intron	N/A	ENSP00000283629.3
	UBP1	ENST00000283628.9	TSL:2	c.114-5704A>G		intron	N/A	ENSP00000283628.5
	UBP1	ENST00000908179.1		c.114-5704A>G		intron	N/A	ENSP00000578238.1

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39132 AN: 151812 Hom.: 5925 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.258 AC: 39195 AN: 151930 Hom.: 5952 Cov.: 32 AF XY: 0.264 AC XY: 19603 AN XY: 74234

African (AFR) AF: 0.366 AC: 15165 AN: 41426

American (AMR) AF: 0.344 AC: 5258 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3466

East Asian (EAS) AF: 0.471 AC: 2430 AN: 5154

South Asian (SAS) AF: 0.237 AC: 1142 AN: 4822

European-Finnish (FIN) AF: 0.268 AC: 2819 AN: 10526

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11067 AN: 67948

Other (OTH) AF: 0.260 AC: 547 AN: 2104

Alfa AF: 0.187 Hom.: 1601

Bravo AF: 0.272

Asia WGS AF: 0.385 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.91
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1807844; hg19: chr3-33472937;