rs679563

Positions:

• chr1-7911018-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011540537.3(UTS2):​c.-75+2163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 150,616 control chromosomes in the GnomAD database, including 27,242 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 0.59 (27242 hom., cov: 28)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+2163C>T		intron_variant			XP_011538839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.591 AC: 88972 AN: 150496 Hom.: 27208 Cov.: 28

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.591 AC: 89062 AN: 150616 Hom.: 27242 Cov.: 28 AF XY: 0.598 AC XY: 43950 AN XY: 73528

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.603

Alfa AF: 0.523 Hom.: 28797

Bravo AF: 0.607

Asia WGS AF: 0.816 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs679563; hg19: chr1-7971078;