chr1-7848828-G-A

Position:

• chr1-7848828-G-A

Variant summary

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

The NM_006786.4(UTS2):​c.258+812C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,072 control chromosomes in the GnomAD database, including 5,123 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 0.25 (5123 hom., cov: 32)
• Consequence: UTS2 NM_006786.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTS2	NM_006786.4	c.258+812C>T		intron_variant		ENST00000361696.10	NP_006777.1
UTS2	NM_021995.2	c.303+812C>T		intron_variant			NP_068835.1
UTS2	XM_011540537.3	c.303+812C>T		intron_variant			XP_011538839.1
UTS2	XM_011540538.2	c.258+812C>T		intron_variant			XP_011538840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTS2	ENST00000361696.10	c.258+812C>T		intron_variant		1	NM_006786.4	ENSP00000355163	P2
UTS2	ENST00000054668.5	c.303+812C>T		intron_variant		1		ENSP00000054668	A2
UTS2	ENST00000377516.6	c.258+812C>T		intron_variant		5		ENSP00000366738

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38230 AN: 151954 Hom.: 5118 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.252 AC: 38271 AN: 152072 Hom.: 5123 Cov.: 32 AF XY: 0.257 AC XY: 19088 AN XY: 74316

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.262

Alfa AF: 0.267 Hom.: 5828

Bravo AF: 0.258

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs228652; hg19: chr1-7908888;