rs17235507

Variant names:

• chr1-7907127-G-A
• rs17235507
• ENST00000788099.1:n.77+6054C>T

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.77+6054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,018 control chromosomes in the GnomAD database, including 1,484 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 0.12 (1484 hom., cov: 31)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 0 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+6054C>T		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.77+6054C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18296 AN: 151896 Hom.: 1485 Cov.: 31

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.120 AC: 18285 AN: 152018 Hom.: 1484 Cov.: 31 AF XY: 0.120 AC XY: 8917 AN XY: 74282

African (AFR) AF: 0.0305 AC: 1265 AN: 41510

American (AMR) AF: 0.132 AC: 2015 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5158

South Asian (SAS) AF: 0.126 AC: 607 AN: 4814

European-Finnish (FIN) AF: 0.159 AC: 1681 AN: 10540

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11342 AN: 67986

Other (OTH) AF: 0.149 AC: 312 AN: 2096

Alfa AF: 0.138 Hom.: 213

Bravo AF: 0.114

Asia WGS AF: 0.0490 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
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: rs17235507; hg19: chr1-7967187;