chr1-7867921-C-T

Variant names:

• chr1-7867921-C-T
• rs579992
• ENST00000788099.1:n.78-11370G>A

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-11370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,212 control chromosomes in the GnomAD database, including 60,982 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 0.89 (60982 hom., cov: 32)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-74-14416G>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.78-11370G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135945 AN: 152094 Hom.: 60928 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.894 AC: 136056 AN: 152212 Hom.: 60982 Cov.: 32 AF XY: 0.898 AC XY: 66793 AN XY: 74414

African (AFR) AF: 0.849 AC: 35242 AN: 41520

American (AMR) AF: 0.899 AC: 13722 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3277 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4982 AN: 5182

South Asian (SAS) AF: 0.920 AC: 4429 AN: 4814

European-Finnish (FIN) AF: 0.961 AC: 10195 AN: 10610

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61312 AN: 68020

Other (OTH) AF: 0.897 AC: 1897 AN: 2116

Alfa AF: 0.903 Hom.: 104098

Bravo AF: 0.888

Asia WGS AF: 0.933 AC: 3245 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	0.31
DANN	Benign	0.31
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs579992; hg19: chr1-7927981;