rs1040396

Variant names:

• chr1-7892344-G-C
• rs1040396
• XM_011540537.3:c.-75+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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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+20837C>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs1040396;

hg19: chr1-7952404;