rs1220627

Positions:

• chr5-73575238-A-G
• chr5-73575238-A-T

Variant summary

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

The NM_032175.4(UTP15):​c.810-1714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,254 control chromosomes in the GnomAD database, including 2,888 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 0.18 (2888 hom., cov: 32)
• Consequence: UTP15 NM_032175.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

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]

UTP15 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTP15	NM_032175.4	c.810-1714A>G		intron_variant		ENST00000296792.9	NP_115551.2
UTP15	NM_001284430.1	c.753-1714A>G		intron_variant			NP_001271359.1
UTP15	NM_001284431.1	c.240-1714A>G		intron_variant			NP_001271360.1
UTP15	XM_011543680.3	c.810-1714A>G		intron_variant			XP_011541982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP15	ENST00000296792.9	c.810-1714A>G		intron_variant		1	NM_032175.4	ENSP00000296792.4

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27843 AN: 152136 Hom.: 2884 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.183 AC: 27861 AN: 152254 Hom.: 2888 Cov.: 32 AF XY: 0.180 AC XY: 13404 AN XY: 74452

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.177

Alfa AF: 0.147 Hom.: 398

Bravo AF: 0.173

Asia WGS AF: 0.0980 AC: 341 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	4.1
DANN	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1220627; hg19: chr5-72871063;