chr1-7867396-T-G

Variant names:

• chr1-7867396-T-G
• rs500508
• XM_011540537.3:c.-74-13891A>C

Variant summary

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

The ENST00000788099.1(ENSG00000302605):​n.78-10845A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,984 control chromosomes in the GnomAD database, including 34,675 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 0.67 (34675 hom., cov: 31)
• Consequence: ENSG00000302605 ENST00000788099.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 9 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.833 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302605	ENST00000788099.1		n.78-10845A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101092 AN: 151866 Hom.: 34654 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.666 AC: 101148 AN: 151984 Hom.: 34675 Cov.: 31 AF XY: 0.670 AC XY: 49814 AN XY: 74300

African (AFR) AF: 0.496 AC: 20548 AN: 41406

American (AMR) AF: 0.771 AC: 11764 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2958 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3754 AN: 5172

South Asian (SAS) AF: 0.855 AC: 4117 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 7010 AN: 10566

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48561 AN: 67978

Other (OTH) AF: 0.712 AC: 1505 AN: 2114

Alfa AF: 0.677 Hom.: 6646

Bravo AF: 0.664

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs500508; hg19: chr1-7927456;