1-7870494-C-G

Position:

• chr1-7870494-C-G

Variant summary

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

The XM_011540537.3(UTS2):​c.-74-16989G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,116 control chromosomes in the GnomAD database, including 34,867 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 (34867 hom., cov: 33)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

Genes affected

UTS2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTS2	XM_011540537.3	c.-74-16989G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102166 AN: 151998 Hom.: 34817 Cov.: 33

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.672 AC: 102269 AN: 152116 Hom.: 34867 Cov.: 33 AF XY: 0.675 AC XY: 50175 AN XY: 74384

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.638

Alfa AF: 0.646 Hom.: 3784

Bravo AF: 0.681

Asia WGS AF: 0.665 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs228724; hg19: chr1-7930554;