rs4780476

Variant names:

• chr16-12768150-A-C
• rs4780476
• NM_018340.3:c.289+13035T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-12768150-A-C
• chr16-12768150-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018340.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPPED1	NM_018340.3	MANE Select	c.289+13035T>G		intron	N/A	NP_060810.2
	CPPED1	NM_001099455.2		c.289+13035T>G		intron	N/A	NP_001092925.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPPED1	ENST00000381774.9	TSL:1 MANE Select	c.289+13035T>G		intron	N/A	ENSP00000371193.4
	CPPED1	ENST00000433677.6	TSL:1	c.289+13035T>G		intron	N/A	ENSP00000411127.2
	CPPED1	ENST00000261660.4	TSL:2	c.289+13035T>G		intron	N/A	ENSP00000261660.4

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

African (AFR) AF: 0.779 AC: 32325 AN: 41494

American (AMR) AF: 0.585 AC: 8932 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2472 AN: 3470

East Asian (EAS) AF: 0.732 AC: 3783 AN: 5168

South Asian (SAS) AF: 0.702 AC: 3381 AN: 4818

European-Finnish (FIN) AF: 0.710 AC: 7504 AN: 10562

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48040 AN: 67980

Other (OTH) AF: 0.722 AC: 1521 AN: 2108

Alfa AF: 0.708 Hom.: 169048

Bravo AF: 0.705

Asia WGS AF: 0.689 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.68
PhyloP100		0.080
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4780476; hg19: chr16-12862007;