rs228721

Positions:

• chr1-7871528-C-A

Variant summary

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

The XM_011540537.3(UTS2):​c.-74-18023G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,048 control chromosomes in the GnomAD database, including 2,901 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 0.17 (2901 hom., cov: 32)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-18023G>T		intron_variant			XP_011538839.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26044 AN: 151930 Hom.: 2901 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.171 AC: 26048 AN: 152048 Hom.: 2901 Cov.: 32 AF XY: 0.174 AC XY: 12902 AN XY: 74302

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.180

Alfa AF: 0.198 Hom.: 571

Bravo AF: 0.161

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228721; hg19: chr1-7931588;