1-7866482-A-G

Position:

• chr1-7866482-A-G

Variant summary

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

The XM_011540537.3(UTS2):​c.-74-12977T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,956 control chromosomes in the GnomAD database, including 35,427 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 0.67 (35427 hom., cov: 30)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTS2	XM_011540537.3	c.-74-12977T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102478 AN: 151838 Hom.: 35403 Cov.: 30

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.675 AC: 102542 AN: 151956 Hom.: 35427 Cov.: 30 AF XY: 0.680 AC XY: 50486 AN XY: 74270

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.720

Alfa AF: 0.726 Hom.: 82753

Bravo AF: 0.674

Asia WGS AF: 0.747 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs504560; hg19: chr1-7926542;