1-153563851-CG-TT

Variant names:

• chr1-153563851-CG-TT
• NM_005978.4:c.26_27delCGinsAA
• S100A2 p.Ala9Glu

Variant summary

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

The NM_005978.4(S100A2):​c.26_27delCGinsAA​(p.Ala9Glu) variant causes a missense change. 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. A9V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: S100A2 NM_005978.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.66
• Publications: 0 publications found

Genes affected

S100A2 (HGNC:10492): (S100 calcium binding protein A2) The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein may have a tumor suppressor function. Chromosomal rearrangements and altered expression of this gene have been implicated in breast cancer. [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_005978.4. 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
	S100A2	NM_005978.4	MANE Select	c.26_27delCGinsAA	p.Ala9Glu	missense	N/A	NP_005969.2	P29034
	S100A2	NM_001366406.1		c.26_27delCGinsAA	p.Ala9Glu	missense	N/A	NP_001353335.1	Q5RHS7
	S100A2	NM_001366407.1		c.-77_-76delCGinsAA		splice_region	Exon 2 of 3	NP_001353336.1	R4GN49

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	S100A2	ENST00000368708.9	TSL:1 MANE Select	c.26_27delCGinsAA	p.Ala9Glu	missense	N/A	ENSP00000357697.4	P29034
	S100A2	ENST00000487430.7	TSL:1	c.26_27delCGinsAA	p.Ala9Glu	missense	N/A	ENSP00000473260.2	P29034
	S100A2	ENST00000368709.6	TSL:3	c.26_27delCGinsAA	p.Ala9Glu	missense	N/A	ENSP00000357698.2	P29034

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		4.7

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: chr1-153536327;