rs8079308

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_213607.3(CCDC103):c.*4G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,533,062 control chromosomes in the GnomAD database, including 56,859 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5267 hom., cov: 31)

Exomes 𝑓: 0.27 ( 51592 hom. )

Consequence

CCDC103
NM_213607.3 3_prime_UTR

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.198

Variant links:

Genes affected

CCDC103 (HGNC:32700): (coiled-coil domain containing 103) Enables protein homodimerization activity. Involved in axonemal dynein complex assembly; cilium movement; and determination of left/right symmetry. Predicted to be located in axoneme. Predicted to be part of outer dynein arm. Implicated in primary ciliary dyskinesia 17. [provided by Alliance of Genome Resources, Apr 2022]

CCDC103 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 17-44902821-G-A is Benign according to our data. Variant chr17-44902821-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 263317.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-44902821-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC103	NM_213607.3 link	c.*4G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000417826.3	NP_998772.1	Q8IW40-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC103	ENST00000417826.3 link	c.*4G>A	3_prime_UTR_variant	Exon 4 of 4	1	NM_213607.3	ENSP00000391692.2	Q8IW40-1
CCDC103	ENST00000410006.6 link	c.*4G>A	3_prime_UTR_variant	Exon 4 of 4	2		ENSP00000387252.1	Q8IW40-1
CCDC103	ENST00000357776.6 link	c.*21G>A	downstream_gene_variant		2		ENSP00000350420.2	F8W6J8

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39674

AN:

151720

Hom.:

5262

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.316

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.271

AC:

40562

AN:

149542

Hom.:

5607

AF XY:

0.271

AC XY:

21424

AN XY:

78986

show subpopulations

Gnomad AFR exome

AF:

0.241

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.249

Gnomad EAS exome

AF:

0.262

Gnomad SAS exome

AF:

0.288

Gnomad FIN exome

AF:

0.323

Gnomad NFE exome

AF:

0.279

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.273

AC:

376894

AN:

1381224

Hom.:

51592

Cov.:

AF XY:

0.273

AC XY:

185576

AN XY:

678538

show subpopulations

Gnomad4 AFR exome

AF:

0.234

Gnomad4 AMR exome

AF:

0.226

Gnomad4 ASJ exome

AF:

0.237

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.283

Gnomad4 FIN exome

AF:

0.315

Gnomad4 NFE exome

AF:

0.276

Gnomad4 OTH exome

AF:

0.263

GnomAD4 genome

AF:

0.261

AC:

39701

AN:

151838

Hom.:

5267

Cov.:

AF XY:

0.261

AC XY:

19365

AN XY:

74176

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.240

Gnomad4 EAS

AF:

0.252

Gnomad4 SAS

AF:

0.272

Gnomad4 FIN

AF:

0.316

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.247

Hom.:

2147

Bravo

AF:

0.253

Asia WGS

AF:

0.227

AC:

788

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

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 -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 05, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia 17

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.3

DANN

Benign

0.63

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.

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