rs1220627

Variant names:

• chr5-73575238-A-G
• rs1220627
• NM_032175.4:c.810-1714A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UTP15	NM_032175.4	c.810-1714A>G		intron_variant	Intron 7 of 12	ENST00000296792.9	NP_115551.2
UTP15	NM_001284430.1	c.753-1714A>G		intron_variant	Intron 7 of 12		NP_001271359.1
UTP15	NM_001284431.1	c.240-1714A>G		intron_variant	Intron 6 of 11		NP_001271360.1
UTP15	XM_011543680.3	c.810-1714A>G		intron_variant	Intron 7 of 12		XP_011541982.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTP15	ENST00000296792.9	c.810-1714A>G		intron_variant	Intron 7 of 12	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

African (AFR) AF: 0.114 AC: 4734 AN: 41554

American (AMR) AF: 0.158 AC: 2416 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3472

East Asian (EAS) AF: 0.0411 AC: 213 AN: 5188

South Asian (SAS) AF: 0.123 AC: 596 AN: 4828

European-Finnish (FIN) AF: 0.255 AC: 2702 AN: 10596

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15791 AN: 68004

Other (OTH) AF: 0.177 AC: 374 AN: 2114

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
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1220627; hg19: chr5-72871063;