rs17374781

Variant names:

• chr1-7859303-C-T
• rs17374781
• XM_011540537.3:c.-74-5798G>A

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-2752G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,118 control chromosomes in the GnomAD database, including 1,911 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 0.15 (1911 hom., cov: 32)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• 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]

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 (NFE) allele frequency at 95% confidence interval = 0.181 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.78-2752G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22128 AN: 152000 Hom.: 1911 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.0501

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.145 AC: 22129 AN: 152118 Hom.: 1911 Cov.: 32 AF XY: 0.145 AC XY: 10792 AN XY: 74358

African (AFR) AF: 0.0996 AC: 4134 AN: 41498

American (AMR) AF: 0.0957 AC: 1461 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 315 AN: 3472

East Asian (EAS) AF: 0.0363 AC: 188 AN: 5176

South Asian (SAS) AF: 0.0499 AC: 240 AN: 4810

European-Finnish (FIN) AF: 0.284 AC: 3005 AN: 10566

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12477 AN: 68006

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.161 Hom.: 1003

Bravo AF: 0.130

Asia WGS AF: 0.0630 AC: 222 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	5.4
DANN	Benign	0.73
PhyloP100		0.27

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: rs17374781;

hg19: chr1-7919363;