rs2066978

Variant names:

• chr1-7868699-T-C
• rs2066978
• XM_011540537.3:c.-74-15194A>G

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-12148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,234 control chromosomes in the GnomAD database, including 2,794 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 0.17 (2794 hom., cov: 33)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 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.78-12148A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25768 AN: 152116 Hom.: 2787 Cov.: 33

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.169 AC: 25772 AN: 152234 Hom.: 2794 Cov.: 33 AF XY: 0.172 AC XY: 12823 AN XY: 74422

African (AFR) AF: 0.0410 AC: 1705 AN: 41556

American (AMR) AF: 0.145 AC: 2213 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.173 AC: 898 AN: 5176

South Asian (SAS) AF: 0.265 AC: 1276 AN: 4824

European-Finnish (FIN) AF: 0.252 AC: 2665 AN: 10594

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15340 AN: 68008

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.194 Hom.: 885

Bravo AF: 0.154

Asia WGS AF: 0.215 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.54
PhyloP100		-0.32

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: rs2066978;

hg19: chr1-7928759;

COSMIC: COSV59922727;