chr1-7859303-C-T

Variant names:

• chr1-7859303-C-T
• rs17374781
• ENST00000788099.1:n.78-2752G>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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-5798G>A		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.78-2752G>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs17374781; hg19: chr1-7919363;