rs228724

Variant names:

• chr1-7870494-C-G
• rs228724
• XM_011540537.3:c.-74-16989G>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

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]

ENSG00000302605 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788099.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000302605	ENST00000788099.1		n.78-13943G>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs228724;

hg19: chr1-7930554;