12-101293265-C-T

Position:

• chr12-101293265-C-T

Variant summary

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

The NM_014503.3(UTP20):​c.1251+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 1,605,336 control chromosomes in the GnomAD database, including 121,286 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 0.33 (9156 hom., cov: 33)
  • Exomes 𝑓: 0.39 (112130 hom.)
• Consequence: UTP20 NM_014503.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTP20	NM_014503.3	c.1251+20C>T		intron_variant		ENST00000261637.5	NP_055318.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP20	ENST00000261637.5	c.1251+20C>T		intron_variant		1	NM_014503.3	ENSP00000261637	P1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49948 AN: 151938 Hom.: 9148 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.375

GnomAD3 exomes AF: 0.376 AC: 93488 AN: 248758 Hom.: 18158 AF XY: 0.384 AC XY: 51603 AN XY: 134516

Gnomad AFR exome AF: 0.153

Gnomad AMR exome AF: 0.369

Gnomad ASJ exome AF: 0.456

Gnomad EAS exome AF: 0.393

Gnomad SAS exome AF: 0.424

Gnomad FIN exome AF: 0.313

Gnomad NFE exome AF: 0.397

Gnomad OTH exome AF: 0.401

GnomAD4 exome AF: 0.389 AC: 565548 AN: 1453280 Hom.: 112130 Cov.: 29 AF XY: 0.391 AC XY: 283202 AN XY: 723384

Gnomad4 AFR exome AF: 0.154

Gnomad4 AMR exome AF: 0.372

Gnomad4 ASJ exome AF: 0.455

Gnomad4 EAS exome AF: 0.411

Gnomad4 SAS exome AF: 0.421

Gnomad4 FIN exome AF: 0.312

Gnomad4 NFE exome AF: 0.395

Gnomad4 OTH exome AF: 0.393

GnomAD4 genome AF: 0.329 AC: 49985 AN: 152056 Hom.: 9156 Cov.: 33 AF XY: 0.329 AC XY: 24432 AN XY: 74330

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.377

Alfa AF: 0.367 Hom.: 5692

Bravo AF: 0.325

Asia WGS AF: 0.402 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.59

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: rs2290720; hg19: chr12-101687043; COSMIC: COSV55374270; COSMIC: COSV55374270;