XM_011540537.3:c.-74-612C>T

Variant names:

• chr1-7854117-G-A
• rs228647
• XM_011540537.3:c.-74-612C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011540537.3(UTS2):​c.-74-612C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,480 control chromosomes in the GnomAD database, including 20,432 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 0.51 (20432 hom., cov: 30)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 5 publications found

Genes affected

UTS2 (HGNC:12636): (urotensin 2) This gene encodes a mature peptide that is an active cyclic heptapeptide absolutely conserved from lamprey to human. The active peptide acts as a vasoconstrictor and is expressed only in brain tissue. Despite the gene family name similarity, this gene is not homologous to urocortin, a member of the sauvagine/corticotropin-releasing factor/urotensin I family. Most of the proprotein is cleaved to make the mature peptide. Transcript variants encoding different preproprotein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-612C>T		intron_variant	Intron 1 of 5		XP_011538839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77660 AN: 151362 Hom.: 20421 Cov.: 30

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.513 AC: 77699 AN: 151480 Hom.: 20432 Cov.: 30 AF XY: 0.508 AC XY: 37620 AN XY: 74028

African (AFR) AF: 0.452 AC: 18649 AN: 41238

American (AMR) AF: 0.444 AC: 6755 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2127 AN: 3456

East Asian (EAS) AF: 0.356 AC: 1831 AN: 5146

South Asian (SAS) AF: 0.609 AC: 2928 AN: 4810

European-Finnish (FIN) AF: 0.458 AC: 4805 AN: 10480

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38620 AN: 67814

Other (OTH) AF: 0.548 AC: 1156 AN: 2108

Alfa AF: 0.387 Hom.: 1027

Bravo AF: 0.501

Asia WGS AF: 0.496 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs228647; hg19: chr1-7914177; COSMIC: COSV50013200;