rs3822452

Positions:

• chr5-73566489-A-C
• chr5-73566489-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032175.4(UTP15):​c.-84+577A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,144 control chromosomes in the GnomAD database, including 12,676 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 0.39 (12676 hom., cov: 33)
• Consequence: UTP15 NM_032175.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

UTP15 (HGNC:25758): (UTP15 small subunit processome component) Enables RNA binding activity. Involved in positive regulation of rRNA processing and positive regulation of transcription by RNA polymerase I. Located in endoplasmic reticulum and fibrillar center. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTP15	NM_032175.4	c.-84+577A>C		intron_variant		ENST00000296792.9
UTP15	NM_001284430.1	c.-84+577A>C		intron_variant
UTP15	NM_001284431.1	c.-481+577A>C		intron_variant
UTP15	XM_011543680.3	c.-84+303A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTP15	ENST00000296792.9	c.-84+577A>C		intron_variant		1	NM_032175.4	P1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59304 AN: 152026 Hom.: 12672 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.390 AC: 59334 AN: 152144 Hom.: 12676 Cov.: 33 AF XY: 0.400 AC XY: 29764 AN XY: 74380

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.418

Alfa AF: 0.330 Hom.: 1327

Bravo AF: 0.390

Asia WGS AF: 0.576 AC: 2004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.7
DANN	Benign	0.62

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: rs3822452; hg19: chr5-72862314;