12-101293265-C-T

Variant names:

• chr12-101293265-C-T
• rs2290720
• NM_014503.3:c.1251+20C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014503.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP20	NM_014503.3	MANE Select	c.1251+20C>T		intron	N/A	NP_055318.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP20	ENST00000261637.5	TSL:1 MANE Select	c.1251+20C>T		intron	N/A	ENSP00000261637.4
	UTP20	ENST00000923497.1		c.1251+20C>T		intron	N/A	ENSP00000593556.1
	UTP20	ENST00000923496.1		c.1251+20C>T		intron	N/A	ENSP00000593555.1

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

GnomAD2 exomes AF: 0.376 AC: 93488 AN: 248758 AF XY: 0.384

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 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

African (AFR) AF: 0.154 AC: 5101 AN: 33230

American (AMR) AF: 0.372 AC: 16536 AN: 44408

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 11866 AN: 26058

East Asian (EAS) AF: 0.411 AC: 16279 AN: 39628

South Asian (SAS) AF: 0.421 AC: 36109 AN: 85744

European-Finnish (FIN) AF: 0.312 AC: 16426 AN: 52628

Middle Eastern (MID) AF: 0.443 AC: 2533 AN: 5724

European-Non Finnish (NFE) AF: 0.395 AC: 437074 AN: 1105696

Other (OTH) AF: 0.393 AC: 23624 AN: 60164

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

African (AFR) AF: 0.158 AC: 6535 AN: 41482

American (AMR) AF: 0.396 AC: 6048 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1595 AN: 3472

East Asian (EAS) AF: 0.395 AC: 2048 AN: 5180

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4824

European-Finnish (FIN) AF: 0.308 AC: 3243 AN: 10534

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27149 AN: 67954

Other (OTH) AF: 0.377 AC: 796 AN: 2114

Alfa AF: 0.368 Hom.: 22198

Bravo AF: 0.325

Asia WGS AF: 0.402 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.59
PhyloP100		-0.10
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: rs2290720; hg19: chr12-101687043; COSMIC: COSV55374270; COSMIC: COSV55374270;