1-209846479-A-G

Position:

• chr1-209846479-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
UTP25	NM_014388.7	c.2027+2783A>G		intron_variant		ENST00000491415.7	NP_055203.4
UTP25	XM_006711275.4	c.1668+4032A>G		intron_variant			XP_006711338.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP25	ENST00000491415.7	c.2027+2783A>G		intron_variant		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

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.782

Alfa AF: 0.779 Hom.: 57028

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

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: rs126280; hg19: chr1-210019824;