chr1-7911018-G-A

Variant names:

• chr1-7911018-G-A
• rs679563
• ENST00000788099.1:n.77+2163C>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+2163C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 150,616 control chromosomes in the GnomAD database, including 27,242 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 0.59 (27242 hom., cov: 28)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 15 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+2163C>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+2163C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.591 AC: 88972 AN: 150496 Hom.: 27208 Cov.: 28

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.591 AC: 89062 AN: 150616 Hom.: 27242 Cov.: 28 AF XY: 0.598 AC XY: 43950 AN XY: 73528

African (AFR) AF: 0.695 AC: 28544 AN: 41096

American (AMR) AF: 0.667 AC: 10098 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1768 AN: 3444

East Asian (EAS) AF: 0.918 AC: 4689 AN: 5108

South Asian (SAS) AF: 0.729 AC: 3438 AN: 4718

European-Finnish (FIN) AF: 0.477 AC: 4951 AN: 10384

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33547 AN: 67446

Other (OTH) AF: 0.603 AC: 1257 AN: 2084

Alfa AF: 0.534 Hom.: 67834

Bravo AF: 0.607

Asia WGS AF: 0.816 AC: 2836 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	0.94
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs679563; hg19: chr1-7971078;