Genetic Variant CNPY3:p.Leu25dup (chr6-42929619-T-TTGC) – ACMG Classification: Likely_benign (-3 pts)

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP6BS1

The NM_006586.5(CNPY3):c.74_76dupTGC(p.Leu25dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000733 in 1,560,544 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00076 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00073 ( 0 hom. )

Consequence

CNPY3
NM_006586.5 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.420

Variant links:

Genes affected

CNPY3 (HGNC:11968): (canopy FGF signaling regulator 3) This gene encodes a protein that binds members of the toll-like receptor protein family and functions as a chaperone to aid in folding and export of these proteins. Alternative splicing results in multiple transcript variants. Naturally occuring readthrough transcription occurs between this locus and the downstream GNMT (glycine N-methyltransferase) gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]

CNPY3 links:

CNPY3-GNMT (HGNC:):

CNPY3-GNMT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 6-42929619-T-TTGC is Benign according to our data. Variant chr6-42929619-T-TTGC is described in ClinVar as [Likely_benign]. Clinvar id is 3047364.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000756 (115/152066) while in subpopulation SAS AF= 0.00207 (10/4826). AF 95% confidence interval is 0.00112. There are 0 homozygotes in gnomad4. There are 60 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNPY3	NM_006586.5 link	c.74_76dupTGC	p.Leu25dup	disruptive_inframe_insertion	Exon 1 of 6	ENST00000372836.5	NP_006577.2	Q9BT09-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNPY3	ENST00000372836.5 link	c.74_76dupTGC	p.Leu25dup	disruptive_inframe_insertion	Exon 1 of 6	1	NM_006586.5	ENSP00000361926.4		Q9BT09-1
ENSG00000287825	ENST00000667155.3 link	n.-143_-141dupGCA		upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.000750

AC:

114

AN:

151950

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000821

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00193

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000574

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00107

AC:

138

AN:

128598

Hom.:

AF XY:

0.00105

AC XY:

AN XY:

69632

show subpopulations

Gnomad AFR exome

AF:

0.000768

Gnomad AMR exome

AF:

0.00209

Gnomad ASJ exome

AF:

0.000146

Gnomad EAS exome

AF:

0.000642

Gnomad SAS exome

AF:

0.00161

Gnomad FIN exome

AF:

0.0000880

Gnomad NFE exome

AF:

0.000864

Gnomad OTH exome

AF:

0.00190

GnomAD4 exome

AF:

0.000731

AC:

1029

AN:

1408478

Hom.:

Cov.:

AF XY:

0.000766

AC XY:

533

AN XY:

696190

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00158

Gnomad4 ASJ exome

AF:

0.0000396

Gnomad4 EAS exome

AF:

0.000649

Gnomad4 SAS exome

AF:

0.00160

Gnomad4 FIN exome

AF:

0.000210

Gnomad4 NFE exome

AF:

0.000653

Gnomad4 OTH exome

AF:

0.00101

GnomAD4 genome

AF:

0.000756

AC:

115

AN:

152066

Hom.:

Cov.:

AF XY:

0.000807

AC XY:

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.000843

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00193

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.000574

Gnomad4 OTH

AF:

0.00142

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

CNPY3-related disorder

Benign:1

Dec 13, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over