rs2270861

chr12-101342603-A-G

Variant summary

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

The NM_014503.3(UTP20):c.4245+14A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 1,590,188 control chromosomes in the GnomAD database, including 47,029 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 0.23 (4328 hom., cov: 32)
  • Exomes 𝑓: 0.24 (42701 hom.)
• Consequence: UTP20 NM_014503.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

UTP20 (HGNC:17897): (UTP20 small subunit processome component) UTP20 is a component of the U3 small nucleolar RNA (snoRNA) (SNORD3A; MIM 180710) protein complex (U3 snoRNP) and is involved in 18S rRNA processing (Wang et al., 2007 [PubMed 17498821]).[supplied by OMIM, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTP20	NM_014503.3	c.4245+14A>G		intron_variant		ENST00000261637.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTP20	ENST00000261637.5	c.4245+14A>G		intron_variant		1	NM_014503.3	P1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34952 AN: 151966 Hom.: 4313 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.261

GnomAD3 exomes AF: 0.253 AC: 57739 AN: 228314 Hom.: 7794 AF XY: 0.251 AC XY: 30984 AN XY: 123622

Gnomad AFR exome AF: 0.174

Gnomad AMR exome AF: 0.352

Gnomad ASJ exome AF: 0.274

Gnomad EAS exome AF: 0.367

Gnomad SAS exome AF: 0.246

Gnomad FIN exome AF: 0.167

Gnomad NFE exome AF: 0.236

Gnomad OTH exome AF: 0.267

GnomAD4 exome AF: 0.240 AC: 345252 AN: 1438104 Hom.: 42701 Cov.: 31 AF XY: 0.240 AC XY: 171817 AN XY: 715016

Gnomad4 AFR exome AF: 0.172

Gnomad4 AMR exome AF: 0.342

Gnomad4 ASJ exome AF: 0.272

Gnomad4 EAS exome AF: 0.388

Gnomad4 SAS exome AF: 0.242

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.249

GnomAD4 genome AF: 0.230 AC: 35014 AN: 152084 Hom.: 4328 Cov.: 32 AF XY: 0.230 AC XY: 17126 AN XY: 74340

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.260

Alfa AF: 0.234 Hom.: 979

Bravo AF: 0.243

Asia WGS AF: 0.329 AC: 1141 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	1.0
Dann	Benign	0.72
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2270861; hg19: chr12-101736381; COSMIC: COSV55374280;