chr2-68252586-G-GGGCGGAGGCGGGGGCGCGCGCGGGCCGGC

Position:

• chr2-68252586-G-GGGCGGAGGCGGGGGCGCGCGCGGGCCGGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000687213.1(ENSG00000289156):​n.132+853_132+854insGCGGAGGCGGGGGCGCGCGCGGGCCGGCG variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 37)
• Consequence: ENST00000687213.1 intron, non_coding_transcript
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 1.52

Genes affected

(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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985892	XR_001739526.2	n.132+853_132+854insGCGGAGGCGGGGGCGCGCGCGGGCCGGCG		intron_variant, non_coding_transcript_variant
LOC107985892	XR_001739527.2	n.132+853_132+854insGCGGAGGCGGGGGCGCGCGCGGGCCGGCG		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687213.1	n.132+853_132+854insGCGGAGGCGGGGGCGCGCGCGGGCCGGCG		intron_variant, non_coding_transcript_variant
PPP3R1	ENST00000409752.5	c.60+3469_60+3470insGCCGGCCCGCGCGCGCCCCCGCCTCCGCC		intron_variant		3
	ENST00000702914.1	n.132+853_132+854insGCGGAGGCGGGGGCGCGCGCGGGCCGGCG		intron_variant, non_coding_transcript_variant
	ENST00000702987.1	n.47+938_47+939insGCGGAGGCGGGGGCGCGCGCGGGCCGGCG		intron_variant, non_coding_transcript_variant

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

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

literature only

Devine Lab Institute for Genome Sciences, University of Maryland School of Medicine

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72174030; hg19: chr2-68479718;