1-7901146-C-T

Variant names:

• chr1-7901146-C-T
• rs227163
• ENST00000788099.1:n.77+12035G>A

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.77+12035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,084 control chromosomes in the GnomAD database, including 32,223 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 0.65 (32223 hom., cov: 33)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 30 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+12035G>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.77+12035G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98010 AN: 151966 Hom.: 32174 Cov.: 33

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.645 AC: 98118 AN: 152084 Hom.: 32223 Cov.: 33 AF XY: 0.645 AC XY: 47955 AN XY: 74312

African (AFR) AF: 0.745 AC: 30931 AN: 41520

American (AMR) AF: 0.688 AC: 10500 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2091 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3691 AN: 5174

South Asian (SAS) AF: 0.559 AC: 2692 AN: 4812

European-Finnish (FIN) AF: 0.647 AC: 6827 AN: 10554

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39548 AN: 67978

Other (OTH) AF: 0.626 AC: 1319 AN: 2108

Alfa AF: 0.601 Hom.: 109421

Bravo AF: 0.655

Asia WGS AF: 0.651 AC: 2262 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	1.8
DANN	Benign	0.55
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs227163; hg19: chr1-7961206;