rs1040396

Positions:

• chr1-7892344-G-C

Variant summary

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

The XM_011540537.3(UTS2):​c.-75+20837C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,782 control chromosomes in the GnomAD database, including 6,234 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 0.26 (6234 hom., cov: 30)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTS2	XM_011540537.3	c.-75+20837C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40179 AN: 151664 Hom.: 6228 Cov.: 30

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.265 AC: 40192 AN: 151782 Hom.: 6234 Cov.: 30 AF XY: 0.266 AC XY: 19695 AN XY: 74170

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.0608

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.238

Alfa AF: 0.314 Hom.: 1135

Bravo AF: 0.244

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1040396; hg19: chr1-7952404;