rs228721

Variant names:

• chr1-7871528-C-A
• rs228721
• XM_011540537.3:c.-74-18023G>T

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-14977G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,048 control chromosomes in the GnomAD database, including 2,901 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 0.17 (2901 hom., cov: 32)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 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.78-14977G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26044 AN: 151930 Hom.: 2901 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.171 AC: 26048 AN: 152048 Hom.: 2901 Cov.: 32 AF XY: 0.174 AC XY: 12902 AN XY: 74302

African (AFR) AF: 0.0429 AC: 1781 AN: 41516

American (AMR) AF: 0.210 AC: 3205 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5176

South Asian (SAS) AF: 0.276 AC: 1325 AN: 4804

European-Finnish (FIN) AF: 0.234 AC: 2468 AN: 10540

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15566 AN: 67972

Other (OTH) AF: 0.180 AC: 379 AN: 2108

Alfa AF: 0.193 Hom.: 573

Bravo AF: 0.161

Asia WGS AF: 0.128 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		0.29

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: rs228721;

hg19: chr1-7931588;