7-5882597-AGC-TCT

Variant names:

• chr7-5882597-AGC-TCT
• NM_001097622.2:c.166_168delAGCinsTCT
• OCM p.57

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_001097622.2(OCM):​c.166_168delAGCinsTCT​(p.57) variant causes a synonymous change involving the alteration of a 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. Synonymous variant affecting the same amino acid position (i.e. S56S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: OCM NM_001097622.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.90
• Publications: 0 publications found

Genes affected

OCM (HGNC:8105): (oncomodulin) Oncomodulin is a high-affinity calcium ion-binding protein. It belongs to the superfamily of calmodulin proteins, also known as the EF-hand proteins. Oncomodulin is an oncodevelopmental protein found in early embryonic cells in the placenta and also in tumors. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001097622.2. 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
	OCM	NM_001097622.2	MANE Select	c.166_168delAGCinsTCT	p.57	synonymous	N/A	NP_001091091.1	P0CE72
	OCM	NM_001391990.1		c.166_168delAGCinsTCT	p.57	synonymous	N/A	NP_001378919.1	P0CE72
	OCM	NM_001391991.1		c.52_54delAGCinsTCT	p.19	synonymous	N/A	NP_001378920.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OCM	ENST00000242104.6	TSL:1 MANE Select	c.166_168delAGCinsTCT	p.57	synonymous	N/A	ENSP00000242104.5	P0CE72
	OCM	ENST00000416608.5	TSL:5	c.166_168delAGCinsTCT	p.57	synonymous	N/A	ENSP00000401365.1	P0CE72

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.9

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: chr7-5922228;