rs665244

Positions:

• chr1-7910188-C-A
• chr1-7910188-C-G
• chr1-7910188-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.-75+2993G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,150 control chromosomes in the GnomAD database, including 246 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 0.050 (246 hom., cov: 31)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.071 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTS2	XM_011540537.3	c.-75+2993G>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7563 AN: 152032 Hom.: 246 Cov.: 31

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.0451

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

GnomAD4 genome AF: 0.0497 AC: 7567 AN: 152150 Hom.: 246 Cov.: 31 AF XY: 0.0498 AC XY: 3702 AN XY: 74382

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.0401

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0488

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.0446

Alfa AF: 0.0175 Hom.: 13

Bravo AF: 0.0463

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665244; hg19: chr1-7970248;