chr1-7892367-G-A

Variant names:

• chr1-7892367-G-A
• rs1040397
• ENST00000788099.1:n.77+20814C>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+20814C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,508 control chromosomes in the GnomAD database, including 6,217 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 0.26 (6217 hom., cov: 30)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+20814C>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+20814C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40130 AN: 151416 Hom.: 6212 Cov.: 30

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.265 AC: 40140 AN: 151508 Hom.: 6217 Cov.: 30 AF XY: 0.266 AC XY: 19664 AN XY: 73980

African (AFR) AF: 0.129 AC: 5328 AN: 41304

American (AMR) AF: 0.248 AC: 3778 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 819 AN: 3460

East Asian (EAS) AF: 0.0608 AC: 313 AN: 5144

South Asian (SAS) AF: 0.261 AC: 1252 AN: 4792

European-Finnish (FIN) AF: 0.443 AC: 4621 AN: 10442

Middle Eastern (MID) AF: 0.118 AC: 34 AN: 288

European-Non Finnish (NFE) AF: 0.343 AC: 23295 AN: 67850

Other (OTH) AF: 0.239 AC: 501 AN: 2100

Alfa AF: 0.315 Hom.: 25397

Bravo AF: 0.245

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.41
PhyloP100		-0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1040397; hg19: chr1-7952427;