1-7849676-AC-GT

Variant names:

• chr1-7849676-AC-GT
• NM_006786.4:c.221_222delGTinsAC
• UTS2 p.Ser74Asn

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_006786.4(UTS2):​c.221_222delGTinsAC​(p.Ser74Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S74G) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: UTS2 NM_006786.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 0 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006786.4. 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
	UTS2	NM_006786.4	MANE Select	c.221_222delGTinsAC	p.Ser74Asn	missense	N/A	NP_006777.1	O95399-1
	UTS2	NM_021995.2		c.266_267delGTinsAC	p.Ser89Asn	missense	N/A	NP_068835.1	O95399-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTS2	ENST00000361696.10	TSL:1 MANE Select	c.221_222delGTinsAC	p.Ser74Asn	missense	N/A	ENSP00000355163.5	O95399-1
	UTS2	ENST00000054668.5	TSL:1	c.266_267delGTinsAC	p.Ser89Asn	missense	N/A	ENSP00000054668.5	O95399-2
	UTS2	ENST00000377516.6	TSL:5	c.221_222delGTinsAC	p.Ser74Asn	missense	N/A	ENSP00000366738.2	Q5H8X8

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.48

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

hg19: chr1-7909736;