rs228647

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-7854117-G-A
• chr1-7854117-G-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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;