rs679563

Variant names:

• chr1-7911018-G-A
• rs679563
• XM_011540537.3:c.-75+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

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]

ENSG00000302605 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788099.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302605	ENST00000788099.1		n.77+2163C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs679563;

hg19: chr1-7971078;