1-7905220-T-C

Variant names:

• chr1-7905220-T-C
• rs6694557
• XM_011540537.3:c.-75+7961A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011540537.3(UTS2):​c.-75+7961A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.902 in 150,568 control chromosomes in the GnomAD database, including 61,552 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 0.90 (61552 hom., cov: 24)
• Consequence: UTS2 XM_011540537.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+7961A>G		intron_variant	Intron 1 of 5		XP_011538839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.902 AC: 135647 AN: 150450 Hom.: 61487 Cov.: 24

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.967

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.902 AC: 135773 AN: 150568 Hom.: 61552 Cov.: 24 AF XY: 0.904 AC XY: 66415 AN XY: 73450

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.967

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.870

Alfa AF: 0.876 Hom.: 7280

Bravo AF: 0.905

Asia WGS AF: 0.974 AC: 3386 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	0.72
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6694557; hg19: chr1-7965280;