1-7884204-A-G

Variant names:

• chr1-7884204-A-G
• rs228703
• ENST00000788099.1:n.78-27653T>C

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-27653T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,028 control chromosomes in the GnomAD database, including 9,622 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 0.34 (9622 hom., cov: 32)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+28977T>C		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.78-27653T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51970 AN: 151912 Hom.: 9626 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.342 AC: 51983 AN: 152028 Hom.: 9622 Cov.: 32 AF XY: 0.341 AC XY: 25321 AN XY: 74308

African (AFR) AF: 0.242 AC: 10023 AN: 41480

American (AMR) AF: 0.363 AC: 5537 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1629 AN: 3472

East Asian (EAS) AF: 0.0406 AC: 210 AN: 5178

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4818

European-Finnish (FIN) AF: 0.361 AC: 3808 AN: 10554

Middle Eastern (MID) AF: 0.407 AC: 118 AN: 290

European-Non Finnish (NFE) AF: 0.402 AC: 27299 AN: 67968

Other (OTH) AF: 0.369 AC: 779 AN: 2110

Alfa AF: 0.386 Hom.: 33320

Bravo AF: 0.332

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs228703; hg19: chr1-7944264;