XM_011540537.3:c.-75+2993G>T

Variant names:

• chr1-7910188-C-A
• rs665244
• XM_011540537.3:c.-75+2993G>T

Variant summary

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

The XM_011540537.3(UTS2):​c.-75+2993G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0497 in 152,150 control chromosomes in the GnomAD database, including 246 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 0.050 (246 hom., cov: 31)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 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 = 0.071 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+2993G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7563 AN: 152032 Hom.: 246 Cov.: 31

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.0451

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

GnomAD4 genome AF: 0.0497 AC: 7567 AN: 152150 Hom.: 246 Cov.: 31 AF XY: 0.0498 AC XY: 3702 AN XY: 74382

African (AFR) AF: 0.0128 AC: 533 AN: 41522

American (AMR) AF: 0.0401 AC: 613 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.0488 AC: 235 AN: 4820

European-Finnish (FIN) AF: 0.0645 AC: 684 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0727 AC: 4945 AN: 67986

Other (OTH) AF: 0.0446 AC: 94 AN: 2108

Alfa AF: 0.0298 Hom.: 46

Bravo AF: 0.0463

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.18
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs665244; hg19: chr1-7970248;