rs1807844

Positions:

• chr3-33431445-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBP1	NM_014517.5	c.114-5704A>G		intron_variant		ENST00000283629.8	NP_055332.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBP1	ENST00000283629.8	c.114-5704A>G		intron_variant		1	NM_014517.5	ENSP00000283629	P3

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

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.260

Alfa AF: 0.187 Hom.: 1412

Bravo AF: 0.272

Asia WGS AF: 0.385 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs1807844; hg19: chr3-33472937;