rs228724

Variant names:

• chr1-7870494-C-G
• rs228724
• ENST00000788099.1:n.78-13943G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-7870494-C-G
• chr1-7870494-C-T

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-13943G>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: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 3 publications found

Genes affected

ENSG00000302605 (HGNC:):

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=-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 rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-16989G>C		intron_variant	Intron 1 of 5		XP_011538839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302605	ENST00000788099.1	n.78-13943G>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.772 AC: 32046 AN: 41500

American (AMR) AF: 0.707 AC: 10825 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3470

East Asian (EAS) AF: 0.739 AC: 3825 AN: 5174

South Asian (SAS) AF: 0.579 AC: 2790 AN: 4820

European-Finnish (FIN) AF: 0.688 AC: 7275 AN: 10574

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41438 AN: 67956

Other (OTH) AF: 0.638 AC: 1349 AN: 2114

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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs228724; hg19: chr1-7930554;