rs2292283

Positions:

• chr5-134227627-A-G
• chr5-134227627-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602919.1(PPP2CA-DT):​n.1218A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,262 control chromosomes in the GnomAD database, including 58,467 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.87 (58466 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: PPP2CA-DT ENST00000602919.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

Genes affected

PPP2CA-DT (HGNC:55266): (PPP2CA divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP2CA-DT	ENST00000602919.1	n.1218A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132928 AN: 152138 Hom.: 58418 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.879

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.874 AC: 133031 AN: 152256 Hom.: 58466 Cov.: 32 AF XY: 0.869 AC XY: 64689 AN XY: 74424

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.879

Alfa AF: 0.881 Hom.: 102827

Bravo AF: 0.867

Asia WGS AF: 0.779 AC: 2710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2292283; hg19: chr5-133563318;