rs4908486

Positions:

• chr1-7854775-C-T

Variant summary

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

The XM_011540537.3(UTS2):​c.-74-1270G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,956 control chromosomes in the GnomAD database, including 6,372 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 0.28 (6372 hom., cov: 31)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTS2	XM_011540537.3	c.-74-1270G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42043 AN: 151838 Hom.: 6367 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.277 AC: 42051 AN: 151956 Hom.: 6372 Cov.: 31 AF XY: 0.279 AC XY: 20700 AN XY: 74258

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.0601

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.260

Alfa AF: 0.295 Hom.: 1724

Bravo AF: 0.257

Asia WGS AF: 0.158 AC: 550 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	2.2
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4908486; hg19: chr1-7914835;