rs4780476

chr16-12768150-A-Cchr16-12768150-A-G

Variant summary

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

The NM_018340.3(CPPED1):c.289+13035T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,072 control chromosomes in the GnomAD database, including 39,155 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 0.72 (39155 hom., cov: 32)
• Consequence: CPPED1 NM_018340.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

Genes affected

CPPED1 (HGNC:25632): (calcineurin like phosphoesterase domain containing 1) Predicted to enable metal ion binding activity; protein serine phosphatase activity; and protein threonine phosphatase activity. Predicted to be involved in protein dephosphorylation. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPPED1	NM_018340.3	c.289+13035T>G		intron_variant		ENST00000381774.9
CPPED1	NM_001099455.2	c.289+13035T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPPED1	ENST00000381774.9	c.289+13035T>G		intron_variant		1	NM_018340.3	P1
CPPED1	ENST00000433677.6	c.289+13035T>G		intron_variant		1
CPPED1	ENST00000261660.4	c.289+13035T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108704 AN: 151954 Hom.: 39118 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.715 AC: 108783 AN: 152072 Hom.: 39155 Cov.: 32 AF XY: 0.713 AC XY: 53014 AN XY: 74330

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.722

Alfa AF: 0.707 Hom.: 75539

Bravo AF: 0.705

Asia WGS AF: 0.689 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.0
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4780476; hg19: chr16-12862007;