1-209846479-A-G

Variant names:

• chr1-209846479-A-G
• rs126280
• NM_014388.7:c.2027+2783A>G

Variant summary

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

The NM_014388.7(UTP25):​c.2027+2783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,062 control chromosomes in the GnomAD database, including 47,697 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 0.79 (47697 hom., cov: 30)
• Consequence: UTP25 NM_014388.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 17 publications found

Genes affected

UTP25 (HGNC:28440): (UTP25 small subunit processome component) Enables RNA binding activity. Involved in several processes, including protein catabolic process; protein destabilization; and protein localization to nucleolus. Located in nucleolus. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTP25	NM_014388.7	c.2027+2783A>G		intron_variant	Intron 11 of 11	ENST00000491415.7	NP_055203.4
UTP25	XM_006711275.4	c.1668+4032A>G		intron_variant	Intron 9 of 9		XP_006711338.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTP25	ENST00000491415.7	c.2027+2783A>G		intron_variant	Intron 11 of 11	1	NM_014388.7	ENSP00000419005.1

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120306 AN: 151944 Hom.: 47664 Cov.: 30

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.792 AC: 120398 AN: 152062 Hom.: 47697 Cov.: 30 AF XY: 0.790 AC XY: 58682 AN XY: 74314

African (AFR) AF: 0.824 AC: 34157 AN: 41474

American (AMR) AF: 0.808 AC: 12350 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2655 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4101 AN: 5142

South Asian (SAS) AF: 0.768 AC: 3700 AN: 4818

European-Finnish (FIN) AF: 0.760 AC: 8043 AN: 10580

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52730 AN: 67982

Other (OTH) AF: 0.782 AC: 1649 AN: 2110

Alfa AF: 0.779 Hom.: 71208

Bravo AF: 0.793

Asia WGS AF: 0.753 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		-2.2
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: rs126280; hg19: chr1-210019824;