rs2066980

Variant names:

• chr1-7868121-G-A
• rs2066980
• XM_011540537.3:c.-74-14616C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-7868121-G-A
• chr1-7868121-G-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

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 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.78-11570C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs2066980;

hg19: chr1-7928181;

COSMIC: COSV59922722;