rs4794220

Variant names:

• chr17-51286186-A-G
• rs4794220
• NM_016001.3:c.1328+818A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016001.3(UTP18):​c.1328+818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,138 control chromosomes in the GnomAD database, including 12,757 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 0.37 (12757 hom., cov: 32)
• Consequence: UTP18 NM_016001.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 11 publications found

Genes affected

UTP18 (HGNC:24274): (UTP18 small subunit processome component) Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in nuclear membrane; nucleolus; and nucleoplasm. [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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016001.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP18	NM_016001.3	MANE Select	c.1328+818A>G		intron	N/A	NP_057085.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP18	ENST00000225298.12	TSL:1 MANE Select	c.1328+818A>G		intron	N/A	ENSP00000225298.7
	UTP18	ENST00000932456.1		c.1358+818A>G		intron	N/A	ENSP00000602515.1
	UTP18	ENST00000854755.1		c.1328+818A>G		intron	N/A	ENSP00000524814.1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56808 AN: 152020 Hom.: 12752 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.373 AC: 56813 AN: 152138 Hom.: 12757 Cov.: 32 AF XY: 0.383 AC XY: 28469 AN XY: 74388

African (AFR) AF: 0.113 AC: 4708 AN: 41554

American (AMR) AF: 0.428 AC: 6549 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3114 AN: 5174

South Asian (SAS) AF: 0.563 AC: 2715 AN: 4824

European-Finnish (FIN) AF: 0.510 AC: 5393 AN: 10566

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31186 AN: 67954

Other (OTH) AF: 0.413 AC: 870 AN: 2108

Alfa AF: 0.395 Hom.: 11923

Bravo AF: 0.354

Asia WGS AF: 0.527 AC: 1830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.75
PhyloP100		0.36
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: rs4794220; hg19: chr17-49363547;