chr1-7892344-G-C

Variant names:

• chr1-7892344-G-C
• rs1040396
• ENST00000788099.1:n.77+20837C>G

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.77+20837C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,782 control chromosomes in the GnomAD database, including 6,234 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 0.26 (6234 hom., cov: 30)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 7 publications found

Genes affected

ENSG00000302605 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTS2	XM_011540537.3	c.-75+20837C>G		intron_variant	Intron 1 of 5		XP_011538839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302605	ENST00000788099.1	n.77+20837C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40179 AN: 151664 Hom.: 6228 Cov.: 30

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0605

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.265 AC: 40192 AN: 151782 Hom.: 6234 Cov.: 30 AF XY: 0.266 AC XY: 19695 AN XY: 74170

African (AFR) AF: 0.129 AC: 5326 AN: 41434

American (AMR) AF: 0.249 AC: 3790 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3460

East Asian (EAS) AF: 0.0608 AC: 313 AN: 5146

South Asian (SAS) AF: 0.261 AC: 1254 AN: 4808

European-Finnish (FIN) AF: 0.441 AC: 4639 AN: 10512

Middle Eastern (MID) AF: 0.119 AC: 34 AN: 286

European-Non Finnish (NFE) AF: 0.344 AC: 23315 AN: 67874

Other (OTH) AF: 0.238 AC: 502 AN: 2106

Alfa AF: 0.314 Hom.: 1135

Bravo AF: 0.244

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.82
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1040396; hg19: chr1-7952404;