Genetic Variant CCDC39:c.1363-13dupT (chr3-180647255-T-TA) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_181426.2(CCDC39):c.1363-13dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,244,132 control chromosomes in the GnomAD database, including 4,949 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1558 hom., cov: 29)

Exomes 𝑓: 0.18 ( 3391 hom. )

Consequence

CCDC39
NM_181426.2 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.273

Variant links:

Genes affected

CCDC39 (HGNC:25244): (coiled-coil domain 39 molecular ruler complex subunit) The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]

CCDC39 links:

ENSG00000145075 (HGNC:):

ENSG00000145075 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-180647255-T-TA is Benign according to our data. Variant chr3-180647255-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 344267.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC39	NM_181426.2 link	c.1363-13dupT		intron_variant	Intron 10 of 19	ENST00000476379.6	NP_852091.1	Q9UFE4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC39	ENST00000476379.6 link	c.1363-13_1363-12insT		intron_variant	Intron 10 of 19	2	NM_181426.2	ENSP00000417960.2		Q9UFE4-1

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

20333

AN:

144448

Hom.:

1557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0733

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.00578

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.119

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.157

GnomAD3 exomes

AF:

0.228

AC:

17226

AN:

75564

Hom.:

292

AF XY:

0.231

AC XY:

9234

AN XY:

39958

show subpopulations

Gnomad AFR exome

AF:

0.121

Gnomad AMR exome

AF:

0.271

Gnomad ASJ exome

AF:

0.250

Gnomad EAS exome

AF:

0.0433

Gnomad SAS exome

AF:

0.211

Gnomad FIN exome

AF:

0.279

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.259

GnomAD4 exome

AF:

0.182

AC:

199677

AN:

1099620

Hom.:

3391

Cov.:

AF XY:

0.180

AC XY:

97507

AN XY:

541312

show subpopulations

Gnomad4 AFR exome

AF:

0.0906

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.168

Gnomad4 EAS exome

AF:

0.0169

Gnomad4 SAS exome

AF:

0.138

Gnomad4 FIN exome

AF:

0.228

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.173

GnomAD4 genome

AF:

0.141

AC:

20344

AN:

144512

Hom.:

1558

Cov.:

AF XY:

0.144

AC XY:

10090

AN XY:

70110

show subpopulations

Gnomad4 AFR

AF:

0.0732

Gnomad4 AMR

AF:

0.183

Gnomad4 ASJ

AF:

0.143

Gnomad4 EAS

AF:

0.00580

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.156

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary ciliary dyskinesia

Benign:2

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Feb 05, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

3-180647255-TAA-TAAA

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