rs72174030

Variant names:

• chr2-68252586-G-GGGCGGAGGCGGGGGCGCGCGCGGGCCGGC
• rs72174030
• ENST00000406334.3:n.-28+401_-28+402insGCCGGCCCGCGCGCGCCCCCGCCTCCGCC

Variant summary

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

The ENST00000406334.3(ENSG00000273398):​n.-28+401_-28+402insGCCGGCCCGCGCGCGCCCCCGCCTCCGCC variant causes a intron 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 INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 37)
• Consequence: ENSG00000273398 ENST00000406334.3 intron
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 1.52
• Publications: 0 publications found

Genes affected

ENSG00000273398 (HGNC:):

PPP3R1 (HGNC:9317): (protein phosphatase 3 regulatory subunit B, alpha) Enables cyclosporin A binding activity; phosphatase binding activity; and protein domain specific binding activity. Involved in calcineurin-NFAT signaling cascade and positive regulation of transcription by RNA polymerase II. Part of calcineurin complex. Implicated in Alzheimer's disease and dilated cardiomyopathy. [provided by Alliance of Genome Resources, Apr 2022]

PPP3R1-AS1 (HGNC:58298):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000406334.3. 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
	PPP3R1	NM_000945.4	MANE Select	c.-460_-459insGCCGGCCCGCGCGCGCCCCCGCCTCCGCC		upstream_gene	N/A	NP_000936.1	P63098

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273398	ENST00000406334.3	TSL:2	n.-28+401_-28+402insGCCGGCCCGCGCGCGCCCCCGCCTCCGCC		intron	N/A	ENSP00000384974.3	H7BYZ3
	PPP3R1	ENST00000409752.5	TSL:3	c.60+3469_60+3470insGCCGGCCCGCGCGCGCCCCCGCCTCCGCC		intron	N/A	ENSP00000387216.1	D3YTA9
	PPP3R1-AS1	ENST00000687213.2		n.187+852_187+853insGGCGGAGGCGGGGGCGCGCGCGGGCCGGC		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 37

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

GnomAD4 genome Cov.: 37

ClinVar

ClinVar submissions

Significance: not provided

Revision: no classification provided

Pathogenic	VUS	Benign	Condition
-	-	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs72174030; hg19: chr2-68479718;