chr5-73566489-A-C

Variant names:

• chr5-73566489-A-C
• rs3822452
• NM_032175.4:c.-84+577A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UTP15	NM_032175.4	c.-84+577A>C		intron_variant	Intron 1 of 12	ENST00000296792.9	NP_115551.2
UTP15	NM_001284430.1	c.-84+577A>C		intron_variant	Intron 1 of 12		NP_001271359.1
UTP15	NM_001284431.1	c.-481+577A>C		intron_variant	Intron 1 of 11		NP_001271360.1
UTP15	XM_011543680.3	c.-84+303A>C		intron_variant	Intron 1 of 12		XP_011541982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTP15	ENST00000296792.9	c.-84+577A>C		intron_variant	Intron 1 of 12	1	NM_032175.4	ENSP00000296792.4

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

African (AFR) AF: 0.224 AC: 9302 AN: 41524

American (AMR) AF: 0.539 AC: 8242 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3472

East Asian (EAS) AF: 0.661 AC: 3411 AN: 5162

South Asian (SAS) AF: 0.559 AC: 2700 AN: 4826

European-Finnish (FIN) AF: 0.452 AC: 4787 AN: 10590

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28158 AN: 67972

Other (OTH) AF: 0.418 AC: 882 AN: 2110

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
PhyloP100		-0.041
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: rs3822452; hg19: chr5-72862314;