chr1-7868121-G-A

Variant names:

• chr1-7868121-G-A
• rs2066980
• ENST00000788099.1:n.78-11570C>T

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-11570C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 141,296 control chromosomes in the GnomAD database, including 28,519 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 (28519 hom., cov: 31)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-14616C>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.78-11570C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 92103 AN: 141204 Hom.: 28494 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.652 AC: 92171 AN: 141296 Hom.: 28519 Cov.: 31 AF XY: 0.653 AC XY: 44817 AN XY: 68654

African (AFR) AF: 0.618 AC: 24054 AN: 38902

American (AMR) AF: 0.562 AC: 7097 AN: 12638

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2195 AN: 3232

East Asian (EAS) AF: 0.578 AC: 2470 AN: 4270

South Asian (SAS) AF: 0.654 AC: 2819 AN: 4310

European-Finnish (FIN) AF: 0.739 AC: 7340 AN: 9938

Middle Eastern (MID) AF: 0.705 AC: 203 AN: 288

European-Non Finnish (NFE) AF: 0.681 AC: 44171 AN: 64878

Other (OTH) AF: 0.663 AC: 1310 AN: 1976

Alfa AF: 0.585 Hom.: 6512

Bravo AF: 0.586

Asia WGS AF: 0.563 AC: 1957 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2066980; hg19: chr1-7928181; COSMIC: COSV59922722;